Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c18d' (ED25519) to the list of known hosts.

You can reproduce this build on your computer by running:

  sudo dnf install copr-rpmbuild
  /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/7524289-epel-9-x86_64 --chroot epel-9-x86_64


Version: 0.73
PID: 7020
Logging PID: 7021
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': False,
 'bootstrap': 'off',
 'build_id': 7524289,
 'buildroot_pkgs': [],
 'chroot': 'epel-9-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': 'cc834df357e4b1d5c93941eace330144d8d98a0a',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/yamaura/genomics/bcftools',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'bcftools',
 'package_version': '1.20-1',
 'project_dirname': 'genomics',
 'project_name': 'genomics',
 'project_owner': 'yamaura',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/yamaura/genomics/epel-9-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'yamaura/genomics--yamaura',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'submitter': 'yamaura',
 'tags': [],
 'task_id': '7524289-epel-9-x86_64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/yamaura/genomics/bcftools /var/lib/copr-rpmbuild/workspace/workdir-4tv0db3h/bcftools --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/yamaura/genomics/bcftools', '/var/lib/copr-rpmbuild/workspace/workdir-4tv0db3h/bcftools', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-4tv0db3h/bcftools'...

Running: git checkout cc834df357e4b1d5c93941eace330144d8d98a0a --

cmd: ['git', 'checkout', 'cc834df357e4b1d5c93941eace330144d8d98a0a', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-4tv0db3h/bcftools
rc: 0
stdout: 
stderr: Note: switching to 'cc834df357e4b1d5c93941eace330144d8d98a0a'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at cc834df automatic import of bcftools

Running: copr-distgit-client sources
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-4tv0db3h/bcftools
rc: 0
stdout: 
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading bcftools-1.20.tar.bz2
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o bcftools-1.20.tar.bz2 --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/yamaura/genomics/bcftools/bcftools-1.20.tar.bz2/md5/5cfb124c7d9e4db6c5a4e6080a2f27f8/bcftools-1.20.tar.bz2
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 7698k  100 7698k    0     0  49.7M      0 --:--:-- --:--:-- --:--:-- 50.1M
INFO: Reading stdout from command: md5sum bcftools-1.20.tar.bz2

Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-4tv0db3h/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-4tv0db3h/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1717414005.411382 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.6 starting (python version = 3.12.1, NVR = mock-5.6-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-4tv0db3h/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-4tv0db3h/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1717414005.411382 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-4tv0db3h/bcftools/bcftools.spec)  Config(rhel+epel-9-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.6
INFO: Mock Version: 5.6
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-x86_64-1717414005.411382/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf detected and used (fallback)
INFO: Buildroot is handled by package management from host and used with --installroot:
  rpm-4.19.1.1-1.fc39.x86_64
  rpm-sequoia-1.6.0-1.fc39.x86_64
  python3-dnf-4.19.2-1.fc39.noarch
  python3-dnf-plugins-core-4.6.0-1.fc39.noarch
  yum-4.19.2-1.fc39.noarch
  dnf5-5.1.17-1.fc39.x86_64
  dnf5-plugins-5.1.17-1.fc39.x86_64
Start: installing minimal buildroot with dnf
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Updating Subscription Management repositories.
Unable to read consumer identity

This system is not registered with an entitlement server. You can use subscription-manager to register.

Copr repository                                 192 kB/s |  17 kB     00:00    
Red Hat Enterprise Linux - BaseOS                17 MB/s |  22 MB     00:01    
Red Hat Enterprise Linux - AppStream             37 MB/s |  35 MB     00:00    
Red Hat Enterprise Linux - CodeReady Linux Buil 9.5 MB/s | 7.8 MB     00:00    
Extra Packages for Enterprise Linux 9 - x86_64   58 MB/s |  21 MB     00:00    
Dependencies resolved.
================================================================================
 Package                     Arch   Version                     Repo       Size
================================================================================
Installing:
 bash                        x86_64 5.1.8-9.el9                 baseos    1.7 M
 bzip2                       x86_64 1.0.8-8.el9                 baseos     60 k
 coreutils                   x86_64 8.32-35.el9                 baseos    1.2 M
 cpio                        x86_64 2.13-16.el9                 baseos    279 k
 diffutils                   x86_64 3.7-12.el9                  baseos    402 k
 epel-rpm-macros             noarch 9-14.el9                    epel       15 k
 findutils                   x86_64 1:4.8.0-6.el9               baseos    550 k
 gawk                        x86_64 5.1.0-6.el9                 baseos    1.0 M
 glibc-minimal-langpack      x86_64 2.34-100.el9_4.2            baseos     28 k
 grep                        x86_64 3.6-5.el9                   baseos    273 k
 gzip                        x86_64 1.12-1.el9                  baseos    167 k
 info                        x86_64 6.7-15.el9                  baseos    228 k
 patch                       x86_64 2.7.6-16.el9                appstream 130 k
 redhat-release              x86_64 9.4-0.4.el9                 baseos     46 k
 redhat-rpm-config           noarch 207-1.el9                   appstream  76 k
 rpm-build                   x86_64 4.16.1.3-29.el9             appstream  72 k
 sed                         x86_64 4.8-9.el9                   baseos    309 k
 tar                         x86_64 2:1.34-6.el9_1              baseos    889 k
 unzip                       x86_64 6.0-56.el9                  baseos    186 k
 util-linux                  x86_64 2.37.4-18.el9               baseos    2.3 M
 which                       x86_64 2.21-29.el9                 baseos     45 k
 xz                          x86_64 5.2.5-8.el9_0               baseos    230 k
Installing dependencies:
 alternatives                x86_64 1.24-1.el9                  baseos     42 k
 ansible-srpm-macros         noarch 1-12.el9                    epel       21 k
 audit-libs                  x86_64 3.1.2-2.el9                 baseos    121 k
 basesystem                  noarch 11-13.el9                   baseos    8.0 k
 binutils                    x86_64 2.35.2-43.el9               baseos    4.6 M
 binutils-gold               x86_64 2.35.2-43.el9               baseos    736 k
 bzip2-libs                  x86_64 1.0.8-8.el9                 baseos     42 k
 ca-certificates             noarch 2023.2.60_v7.0.306-90.1.el9_2
                                                                baseos    846 k
 coreutils-common            x86_64 8.32-35.el9                 baseos    2.0 M
 cracklib                    x86_64 2.9.6-27.el9                baseos     99 k
 cracklib-dicts              x86_64 2.9.6-27.el9                baseos    3.6 M
 crypto-policies             noarch 20240202-1.git283706d.el9   baseos     88 k
 curl                        x86_64 7.76.1-29.el9_4             baseos    298 k
 cyrus-sasl-lib              x86_64 2.1.27-21.el9               baseos    774 k
 debugedit                   x86_64 5.0-5.el9                   appstream  81 k
 dwz                         x86_64 0.14-3.el9                  appstream 130 k
 ed                          x86_64 1.14.2-12.el9               baseos     78 k
 efi-srpm-macros             noarch 6-2.el9_0                   appstream  24 k
 elfutils                    x86_64 0.190-2.el9                 baseos    559 k
 elfutils-debuginfod-client  x86_64 0.190-2.el9                 baseos     39 k
 elfutils-default-yama-scope noarch 0.190-2.el9                 baseos     12 k
 elfutils-libelf             x86_64 0.190-2.el9                 baseos    196 k
 elfutils-libs               x86_64 0.190-2.el9                 baseos    258 k
 file                        x86_64 5.39-16.el9                 baseos     52 k
 file-libs                   x86_64 5.39-16.el9                 baseos    593 k
 filesystem                  x86_64 3.16-2.el9                  baseos    4.7 M
 fonts-srpm-macros           noarch 1:2.0.5-7.el9.1             appstream  29 k
 forge-srpm-macros           noarch 0.3.1-1.el9                 epel       19 k
 fpc-srpm-macros             noarch 1.3-7.el9                   epel      7.5 k
 gdb-minimal                 x86_64 10.2-13.el9                 appstream 3.5 M
 gdbm-libs                   x86_64 1:1.19-4.el9                baseos     56 k
 ghc-srpm-macros             noarch 1.5.0-6.el9                 appstream 9.0 k
 glibc                       x86_64 2.34-100.el9_4.2            baseos    2.0 M
 glibc-common                x86_64 2.34-100.el9_4.2            baseos    313 k
 glibc-gconv-extra           x86_64 2.34-100.el9_4.2            baseos    1.7 M
 gmp                         x86_64 1:6.2.0-13.el9              baseos    319 k
 go-srpm-macros              noarch 3.2.0-3.el9                 appstream  28 k
 go-srpm-macros-epel         noarch 3.3.0.5-1.el9               epel       27 k
 groff-base                  x86_64 1.22.4-10.el9               baseos    1.1 M
 kernel-srpm-macros          noarch 1.0-13.el9                  appstream  17 k
 keyutils-libs               x86_64 1.6.3-1.el9                 baseos     34 k
 krb5-libs                   x86_64 1.21.1-1.el9                baseos    770 k
 libacl                      x86_64 2.3.1-4.el9                 baseos     24 k
 libarchive                  x86_64 3.5.3-4.el9                 baseos    392 k
 libattr                     x86_64 2.5.1-3.el9                 baseos     20 k
 libblkid                    x86_64 2.37.4-18.el9               baseos    110 k
 libbrotli                   x86_64 1.0.9-6.el9                 baseos    317 k
 libcap                      x86_64 2.48-9.el9_2                baseos     74 k
 libcap-ng                   x86_64 0.8.2-7.el9                 baseos     36 k
 libcom_err                  x86_64 1.46.5-5.el9                baseos     28 k
 libcurl                     x86_64 7.76.1-29.el9_4             baseos    286 k
 libdb                       x86_64 5.3.28-53.el9               baseos    740 k
 libeconf                    x86_64 0.4.1-3.el9_2               baseos     30 k
 libevent                    x86_64 2.1.12-6.el9                baseos    268 k
 libfdisk                    x86_64 2.37.4-18.el9               baseos    157 k
 libffi                      x86_64 3.4.2-8.el9                 baseos     40 k
 libgcc                      x86_64 11.4.1-3.el9                baseos     95 k
 libgcrypt                   x86_64 1.10.0-10.el9_2             baseos    508 k
 libgomp                     x86_64 11.4.1-3.el9                baseos    270 k
 libgpg-error                x86_64 1.42-5.el9                  baseos    220 k
 libidn2                     x86_64 2.3.0-7.el9                 baseos    105 k
 libmount                    x86_64 2.37.4-18.el9               baseos    138 k
 libnghttp2                  x86_64 1.43.0-5.el9_4.3            baseos     75 k
 libpkgconf                  x86_64 1.7.3-10.el9                baseos     37 k
 libpsl                      x86_64 0.21.1-5.el9                baseos     66 k
 libpwquality                x86_64 1.4.4-8.el9                 baseos    123 k
 libselinux                  x86_64 3.6-1.el9                   baseos     88 k
 libsemanage                 x86_64 3.6-1.el9                   baseos    121 k
 libsepol                    x86_64 3.6-1.el9                   baseos    331 k
 libsigsegv                  x86_64 2.13-4.el9                  baseos     30 k
 libsmartcols                x86_64 2.37.4-18.el9               baseos     66 k
 libssh                      x86_64 0.10.4-13.el9               baseos    220 k
 libssh-config               noarch 0.10.4-13.el9               baseos     11 k
 libstdc++                   x86_64 11.4.1-3.el9                baseos    747 k
 libtasn1                    x86_64 4.16.0-8.el9_1              baseos     77 k
 libunistring                x86_64 0.9.10-15.el9               baseos    499 k
 libutempter                 x86_64 1.2.1-6.el9                 baseos     30 k
 libuuid                     x86_64 2.37.4-18.el9               baseos     30 k
 libverto                    x86_64 0.3.2-3.el9                 baseos     24 k
 libxcrypt                   x86_64 4.4.18-3.el9                baseos    120 k
 libxml2                     x86_64 2.9.13-6.el9_4              baseos    752 k
 libzstd                     x86_64 1.5.1-2.el9                 baseos    332 k
 lua-libs                    x86_64 5.4.4-4.el9                 baseos    132 k
 lua-srpm-macros             noarch 1-6.el9                     appstream  10 k
 lz4-libs                    x86_64 1.9.3-5.el9                 baseos     69 k
 mpfr                        x86_64 4.1.0-7.el9                 baseos    329 k
 ncurses                     x86_64 6.2-10.20210508.el9         baseos    410 k
 ncurses-base                noarch 6.2-10.20210508.el9         baseos     99 k
 ncurses-libs                x86_64 6.2-10.20210508.el9         baseos    332 k
 ocaml-srpm-macros           noarch 6-6.el9                     appstream 9.1 k
 openblas-srpm-macros        noarch 2-11.el9                    appstream 8.6 k
 openldap                    x86_64 2.6.6-3.el9                 baseos    286 k
 openssl                     x86_64 1:3.0.7-27.el9              baseos    1.2 M
 openssl-fips-provider       x86_64 3.0.7-2.el9                 baseos    576 k
 openssl-libs                x86_64 1:3.0.7-27.el9              baseos    1.9 M
 p11-kit                     x86_64 0.25.3-2.el9                baseos    537 k
 p11-kit-trust               x86_64 0.25.3-2.el9                baseos    145 k
 pam                         x86_64 1.5.1-19.el9                baseos    631 k
 pcre                        x86_64 8.44-3.el9.3                baseos    202 k
 pcre2                       x86_64 10.40-5.el9                 baseos    236 k
 pcre2-syntax                noarch 10.40-5.el9                 baseos    145 k
 perl-AutoLoader             noarch 5.74-481.el9                appstream  21 k
 perl-B                      x86_64 1.80-481.el9                appstream 184 k
 perl-Carp                   noarch 1.50-460.el9                appstream  31 k
 perl-Class-Struct           noarch 0.66-481.el9                appstream  22 k
 perl-Data-Dumper            x86_64 2.174-462.el9               appstream  59 k
 perl-Digest                 noarch 1.19-4.el9                  appstream  29 k
 perl-Digest-MD5             x86_64 2.58-4.el9                  appstream  39 k
 perl-Encode                 x86_64 4:3.08-462.el9              appstream 1.7 M
 perl-Errno                  x86_64 1.30-481.el9                appstream  15 k
 perl-Exporter               noarch 5.74-461.el9                appstream  34 k
 perl-Fcntl                  x86_64 1.13-481.el9                appstream  22 k
 perl-File-Basename          noarch 2.85-481.el9                appstream  17 k
 perl-File-Path              noarch 2.18-4.el9                  appstream  38 k
 perl-File-Temp              noarch 1:0.231.100-4.el9           appstream  63 k
 perl-File-stat              noarch 1.09-481.el9                appstream  17 k
 perl-FileHandle             noarch 2.03-481.el9                appstream  16 k
 perl-Getopt-Long            noarch 1:2.52-4.el9                appstream  64 k
 perl-Getopt-Std             noarch 1.12-481.el9                appstream  16 k
 perl-HTTP-Tiny              noarch 0.076-462.el9               appstream  57 k
 perl-IO                     x86_64 1.43-481.el9                appstream  92 k
 perl-IO-Socket-IP           noarch 0.41-5.el9                  appstream  45 k
 perl-IO-Socket-SSL          noarch 2.073-1.el9                 appstream 223 k
 perl-IPC-Open3              noarch 1.21-481.el9                appstream  24 k
 perl-MIME-Base64            x86_64 3.16-4.el9                  appstream  34 k
 perl-Mozilla-CA             noarch 20200520-6.el9              appstream  14 k
 perl-Net-SSLeay             x86_64 1.92-2.el9                  appstream 392 k
 perl-POSIX                  x86_64 1.94-481.el9                appstream  98 k
 perl-PathTools              x86_64 3.78-461.el9                appstream  92 k
 perl-Pod-Escapes            noarch 1:1.07-460.el9              appstream  22 k
 perl-Pod-Perldoc            noarch 3.28.01-461.el9             appstream  92 k
 perl-Pod-Simple             noarch 1:3.42-4.el9                appstream 229 k
 perl-Pod-Usage              noarch 4:2.01-4.el9                appstream  43 k
 perl-Scalar-List-Utils      x86_64 4:1.56-461.el9              appstream  77 k
 perl-SelectSaver            noarch 1.02-481.el9                appstream  12 k
 perl-Socket                 x86_64 4:2.031-4.el9               appstream  58 k
 perl-Storable               x86_64 1:3.21-460.el9              appstream  98 k
 perl-Symbol                 noarch 1.08-481.el9                appstream  14 k
 perl-Term-ANSIColor         noarch 5.01-461.el9                appstream  51 k
 perl-Term-Cap               noarch 1.17-460.el9                appstream  24 k
 perl-Text-ParseWords        noarch 3.30-460.el9                appstream  18 k
 perl-Text-Tabs+Wrap         noarch 2013.0523-460.el9           appstream  25 k
 perl-Time-Local             noarch 2:1.300-7.el9               appstream  37 k
 perl-URI                    noarch 5.09-3.el9                  appstream 125 k
 perl-base                   noarch 2.27-481.el9                appstream  16 k
 perl-constant               noarch 1.33-461.el9                appstream  25 k
 perl-if                     noarch 0.60.800-481.el9            appstream  14 k
 perl-interpreter            x86_64 4:5.32.1-481.el9            appstream  73 k
 perl-libnet                 noarch 3.13-4.el9                  appstream 134 k
 perl-libs                   x86_64 4:5.32.1-481.el9            appstream 2.2 M
 perl-mro                    x86_64 1.23-481.el9                appstream  29 k
 perl-overload               noarch 1.31-481.el9                appstream  46 k
 perl-overloading            noarch 0.02-481.el9                appstream  13 k
 perl-parent                 noarch 1:0.238-460.el9             appstream  16 k
 perl-podlators              noarch 1:4.14-460.el9              appstream 118 k
 perl-srpm-macros            noarch 1-41.el9                    appstream 9.4 k
 perl-subs                   noarch 1.03-481.el9                appstream  12 k
 perl-vars                   noarch 1.05-481.el9                appstream  13 k
 pkgconf                     x86_64 1.7.3-10.el9                baseos     45 k
 pkgconf-m4                  noarch 1.7.3-10.el9                baseos     16 k
 pkgconf-pkg-config          x86_64 1.7.3-10.el9                baseos     12 k
 popt                        x86_64 1.18-8.el9                  baseos     69 k
 publicsuffix-list-dafsa     noarch 20210518-3.el9              baseos     59 k
 pyproject-srpm-macros       noarch 1.12.0-1.el9                appstream  14 k
 python-srpm-macros          noarch 3.9-53.el9                  appstream  19 k
 qt5-srpm-macros             noarch 5.15.9-1.el9                appstream 9.1 k
 qt6-srpm-macros             noarch 6.6.2-1.el9                 epel      8.7 k
 readline                    x86_64 8.1-4.el9                   baseos    215 k
 rpm                         x86_64 4.16.1.3-29.el9             baseos    541 k
 rpm-build-libs              x86_64 4.16.1.3-29.el9             baseos     90 k
 rpm-libs                    x86_64 4.16.1.3-29.el9             baseos    310 k
 rpmautospec-rpm-macros      noarch 0.6.3-1.el9                 epel      9.9 k
 rust-srpm-macros            noarch 17-4.el9                    appstream  11 k
 rust-srpm-macros-epel       noarch 26.3-1.el9                  epel       10 k
 setup                       noarch 2.13.7-10.el9               baseos    150 k
 shadow-utils                x86_64 2:4.9-8.el9                 baseos    1.2 M
 sqlite-libs                 x86_64 3.34.1-7.el9_3              baseos    622 k
 systemd-libs                x86_64 252-32.el9_4                baseos    679 k
 tzdata                      noarch 2024a-1.el9                 baseos    842 k
 util-linux-core             x86_64 2.37.4-18.el9               baseos    469 k
 xz-libs                     x86_64 5.2.5-8.el9_0               baseos     94 k
 zip                         x86_64 3.0-35.el9                  baseos    270 k
 zlib                        x86_64 1.2.11-40.el9               baseos     93 k
 zstd                        x86_64 1.5.1-2.el9                 baseos    552 k

Transaction Summary
================================================================================
Install  206 Packages

Total download size: 68 M
Installed size: 215 M
Downloading Packages:
(1/206): basesystem-11-13.el9.noarch.rpm         53 kB/s | 8.0 kB     00:00    
(2/206): bzip2-libs-1.0.8-8.el9.x86_64.rpm      236 kB/s |  42 kB     00:00    
(3/206): cracklib-2.9.6-27.el9.x86_64.rpm       876 kB/s |  99 kB     00:00    
(4/206): cpio-2.13-16.el9.x86_64.rpm            1.6 MB/s | 279 kB     00:00    
(5/206): ed-1.14.2-12.el9.x86_64.rpm            825 kB/s |  78 kB     00:00    
(6/206): filesystem-3.16-2.el9.x86_64.rpm        25 MB/s | 4.7 MB     00:00    
(7/206): grep-3.6-5.el9.x86_64.rpm              2.1 MB/s | 273 kB     00:00    
(8/206): info-6.7-15.el9.x86_64.rpm             2.8 MB/s | 228 kB     00:00    
(9/206): groff-base-1.22.4-10.el9.x86_64.rpm    7.9 MB/s | 1.1 MB     00:00    
(10/206): libattr-2.5.1-3.el9.x86_64.rpm        217 kB/s |  20 kB     00:00    
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(14/206): libdb-5.3.28-53.el9.x86_64.rpm        5.2 MB/s | 740 kB     00:00    
(15/206): libgpg-error-1.42-5.el9.x86_64.rpm    2.4 MB/s | 220 kB     00:00    
(16/206): libidn2-2.3.0-7.el9.x86_64.rpm        1.1 MB/s | 105 kB     00:00    
(17/206): libpsl-0.21.1-5.el9.x86_64.rpm        934 kB/s |  66 kB     00:00    
(18/206): libpwquality-1.4.4-8.el9.x86_64.rpm   1.6 MB/s | 123 kB     00:00    
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(20/206): libunistring-0.9.10-15.el9.x86_64.rpm 6.2 MB/s | 499 kB     00:00    
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(26/206): mpfr-4.1.0-7.el9.x86_64.rpm           4.3 MB/s | 329 kB     00:00    
(27/206): pcre-8.44-3.el9.3.x86_64.rpm          2.3 MB/s | 202 kB     00:00    
(28/206): popt-1.18-8.el9.x86_64.rpm            882 kB/s |  69 kB     00:00    
(29/206): publicsuffix-list-dafsa-20210518-3.el 863 kB/s |  59 kB     00:00    
(30/206): sed-4.8-9.el9.x86_64.rpm              3.8 MB/s | 309 kB     00:00    
(31/206): readline-8.1-4.el9.x86_64.rpm         1.3 MB/s | 215 kB     00:00    
(32/206): unzip-6.0-56.el9.x86_64.rpm           2.5 MB/s | 186 kB     00:00    
(33/206): diffutils-3.7-12.el9.x86_64.rpm       4.5 MB/s | 402 kB     00:00    
(34/206): cracklib-dicts-2.9.6-27.el9.x86_64.rp  18 MB/s | 3.6 MB     00:00    
(35/206): gawk-5.1.0-6.el9.x86_64.rpm           9.3 MB/s | 1.0 MB     00:00    
(36/206): xz-5.2.5-8.el9_0.x86_64.rpm           3.1 MB/s | 230 kB     00:00    
(37/206): gdbm-libs-1.19-4.el9.x86_64.rpm       503 kB/s |  56 kB     00:00    
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(39/206): zstd-1.5.1-2.el9.x86_64.rpm           6.2 MB/s | 552 kB     00:00    
(40/206): cyrus-sasl-lib-2.1.27-21.el9.x86_64.r 9.8 MB/s | 774 kB     00:00    
(41/206): gzip-1.12-1.el9.x86_64.rpm            1.6 MB/s | 167 kB     00:00    
(42/206): libtasn1-4.16.0-8.el9_1.x86_64.rpm    943 kB/s |  77 kB     00:00    
(43/206): tar-1.34-6.el9_1.x86_64.rpm            11 MB/s | 889 kB     00:00    
(44/206): ca-certificates-2023.2.60_v7.0.306-90  11 MB/s | 846 kB     00:00    
(45/206): libarchive-3.5.3-4.el9.x86_64.rpm     5.3 MB/s | 392 kB     00:00    
(46/206): keyutils-libs-1.6.3-1.el9.x86_64.rpm  262 kB/s |  34 kB     00:00    
(47/206): libcap-2.48-9.el9_2.x86_64.rpm        896 kB/s |  74 kB     00:00    
(48/206): libeconf-0.4.1-3.el9_2.x86_64.rpm     249 kB/s |  30 kB     00:00    
(49/206): libgcrypt-1.10.0-10.el9_2.x86_64.rpm  6.1 MB/s | 508 kB     00:00    
(50/206): pkgconf-1.7.3-10.el9.x86_64.rpm       644 kB/s |  45 kB     00:00    
(51/206): libpkgconf-1.7.3-10.el9.x86_64.rpm    285 kB/s |  37 kB     00:00    
(52/206): pkgconf-m4-1.7.3-10.el9.noarch.rpm    229 kB/s |  16 kB     00:00    
(53/206): zip-3.0-35.el9.x86_64.rpm             3.7 MB/s | 270 kB     00:00    
(54/206): alternatives-1.24-1.el9.x86_64.rpm    533 kB/s |  42 kB     00:00    
(55/206): pkgconf-pkg-config-1.7.3-10.el9.x86_6  48 kB/s |  12 kB     00:00    
(56/206): findutils-4.8.0-6.el9.x86_64.rpm      6.8 MB/s | 550 kB     00:00    
(57/206): krb5-libs-1.21.1-1.el9.x86_64.rpm     9.7 MB/s | 770 kB     00:00    
(58/206): libffi-3.4.2-8.el9.x86_64.rpm         479 kB/s |  40 kB     00:00    
(59/206): lua-libs-5.4.4-4.el9.x86_64.rpm       1.3 MB/s | 132 kB     00:00    
(60/206): gmp-6.2.0-13.el9.x86_64.rpm           909 kB/s | 319 kB     00:00    
(61/206): ncurses-6.2-10.20210508.el9.x86_64.rp 5.2 MB/s | 410 kB     00:00    
(62/206): ncurses-libs-6.2-10.20210508.el9.x86_ 3.0 MB/s | 332 kB     00:00    
(63/206): ncurses-base-6.2-10.20210508.el9.noar 800 kB/s |  99 kB     00:00    
(64/206): shadow-utils-4.9-8.el9.x86_64.rpm      13 MB/s | 1.2 MB     00:00    
(65/206): which-2.21-29.el9.x86_64.rpm          367 kB/s |  45 kB     00:00    
(66/206): zlib-1.2.11-40.el9.x86_64.rpm         877 kB/s |  93 kB     00:00    
(67/206): audit-libs-3.1.2-2.el9.x86_64.rpm     1.2 MB/s | 121 kB     00:00    
(68/206): bash-5.1.8-9.el9.x86_64.rpm            19 MB/s | 1.7 MB     00:00    
(69/206): binutils-gold-2.35.2-43.el9.x86_64.rp 9.5 MB/s | 736 kB     00:00    
(70/206): binutils-2.35.2-43.el9.x86_64.rpm      23 MB/s | 4.6 MB     00:00    
(71/206): coreutils-8.32-35.el9.x86_64.rpm       15 MB/s | 1.2 MB     00:00    
(72/206): curl-7.76.1-29.el9_4.x86_64.rpm       3.3 MB/s | 298 kB     00:00    
(73/206): coreutils-common-8.32-35.el9.x86_64.r  16 MB/s | 2.0 MB     00:00    
(74/206): elfutils-0.190-2.el9.x86_64.rpm       5.1 MB/s | 559 kB     00:00    
(75/206): elfutils-default-yama-scope-0.190-2.e  70 kB/s |  12 kB     00:00    
(76/206): elfutils-libs-0.190-2.el9.x86_64.rpm  2.5 MB/s | 258 kB     00:00    
(77/206): file-5.39-16.el9.x86_64.rpm           533 kB/s |  52 kB     00:00    
(78/206): file-libs-5.39-16.el9.x86_64.rpm      6.5 MB/s | 593 kB     00:00    
(79/206): libacl-2.3.1-4.el9.x86_64.rpm         349 kB/s |  24 kB     00:00    
(80/206): libblkid-2.37.4-18.el9.x86_64.rpm     1.4 MB/s | 110 kB     00:00    
(81/206): libfdisk-2.37.4-18.el9.x86_64.rpm     2.2 MB/s | 157 kB     00:00    
(82/206): libgcc-11.4.1-3.el9.x86_64.rpm        1.0 MB/s |  95 kB     00:00    
(83/206): libmount-2.37.4-18.el9.x86_64.rpm     1.9 MB/s | 138 kB     00:00    
(84/206): libgomp-11.4.1-3.el9.x86_64.rpm       1.5 MB/s | 270 kB     00:00    
(85/206): libselinux-3.6-1.el9.x86_64.rpm       878 kB/s |  88 kB     00:00    
(86/206): libsemanage-3.6-1.el9.x86_64.rpm      1.7 MB/s | 121 kB     00:00    
(87/206): libsepol-3.6-1.el9.x86_64.rpm         3.0 MB/s | 331 kB     00:00    
(88/206): libsmartcols-2.37.4-18.el9.x86_64.rpm 661 kB/s |  66 kB     00:00    
(89/206): libuuid-2.37.4-18.el9.x86_64.rpm      449 kB/s |  30 kB     00:00    
(90/206): libstdc++-11.4.1-3.el9.x86_64.rpm     5.9 MB/s | 747 kB     00:00    
(91/206): openldap-2.6.6-3.el9.x86_64.rpm       3.7 MB/s | 286 kB     00:00    
(92/206): openssl-3.0.7-27.el9.x86_64.rpm        11 MB/s | 1.2 MB     00:00    
(93/206): openssl-fips-provider-3.0.7-2.el9.x86 5.2 MB/s | 576 kB     00:00    
(94/206): openssl-libs-3.0.7-27.el9.x86_64.rpm   20 MB/s | 1.9 MB     00:00    
(95/206): p11-kit-0.25.3-2.el9.x86_64.rpm       6.9 MB/s | 537 kB     00:00    
(96/206): p11-kit-trust-0.25.3-2.el9.x86_64.rpm 2.0 MB/s | 145 kB     00:00    
(97/206): pam-1.5.1-19.el9.x86_64.rpm           8.0 MB/s | 631 kB     00:00    
(98/206): pcre2-10.40-5.el9.x86_64.rpm          3.0 MB/s | 236 kB     00:00    
(99/206): rpm-4.16.1.3-29.el9.x86_64.rpm        5.4 MB/s | 541 kB     00:00    
(100/206): rpm-build-libs-4.16.1.3-29.el9.x86_6 1.3 MB/s |  90 kB     00:00    
(101/206): rpm-libs-4.16.1.3-29.el9.x86_64.rpm  4.3 MB/s | 310 kB     00:00    
(102/206): setup-2.13.7-10.el9.noarch.rpm       2.0 MB/s | 150 kB     00:00    
(103/206): sqlite-libs-3.34.1-7.el9_3.x86_64.rp 7.0 MB/s | 622 kB     00:00    
(104/206): systemd-libs-252-32.el9_4.x86_64.rpm 8.6 MB/s | 679 kB     00:00    
(105/206): bzip2-1.0.8-8.el9.x86_64.rpm          11 kB/s |  60 kB     00:05    
(106/206): util-linux-2.37.4-18.el9.x86_64.rpm   17 MB/s | 2.3 MB     00:00    
(107/206): tzdata-2024a-1.el9.noarch.rpm        5.8 MB/s | 842 kB     00:00    
(108/206): elfutils-debuginfod-client-0.190-2.e 567 kB/s |  39 kB     00:00    
(109/206): crypto-policies-20240202-1.git283706 847 kB/s |  88 kB     00:00    
(110/206): elfutils-libelf-0.190-2.el9.x86_64.r 2.6 MB/s | 196 kB     00:00    
(111/206): libcom_err-1.46.5-5.el9.x86_64.rpm   380 kB/s |  28 kB     00:00    
(112/206): libcurl-7.76.1-29.el9_4.x86_64.rpm   3.6 MB/s | 286 kB     00:00    
(113/206): libssh-config-0.10.4-13.el9.noarch.r 153 kB/s |  11 kB     00:00    
(114/206): pcre2-syntax-10.40-5.el9.noarch.rpm  1.8 MB/s | 145 kB     00:00    
(115/206): libssh-0.10.4-13.el9.x86_64.rpm      1.1 MB/s | 220 kB     00:00    
(116/206): redhat-release-9.4-0.4.el9.x86_64.rp 636 kB/s |  46 kB     00:00    
(117/206): libxml2-2.9.13-6.el9_4.x86_64.rpm    9.7 MB/s | 752 kB     00:00    
(118/206): glibc-common-2.34-100.el9_4.2.x86_64 3.4 MB/s | 313 kB     00:00    
(119/206): glibc-2.34-100.el9_4.2.x86_64.rpm     14 MB/s | 2.0 MB     00:00    
(120/206): glibc-gconv-extra-2.34-100.el9_4.2.x  14 MB/s | 1.7 MB     00:00    
(121/206): glibc-minimal-langpack-2.34-100.el9_ 284 kB/s |  28 kB     00:00    
(122/206): ghc-srpm-macros-1.5.0-6.el9.noarch.r 100 kB/s | 9.0 kB     00:00    
(123/206): libnghttp2-1.43.0-5.el9_4.3.x86_64.r 653 kB/s |  75 kB     00:00    
(124/206): lua-srpm-macros-1-6.el9.noarch.rpm   147 kB/s |  10 kB     00:00    
(125/206): perl-Data-Dumper-2.174-462.el9.x86_6 862 kB/s |  59 kB     00:00    
(126/206): perl-Digest-MD5-2.58-4.el9.x86_64.rp 380 kB/s |  39 kB     00:00    
(127/206): perl-Encode-3.08-462.el9.x86_64.rpm   12 MB/s | 1.7 MB     00:00    
(128/206): perl-IO-Socket-SSL-2.073-1.el9.noarc 3.1 MB/s | 223 kB     00:00    
(129/206): perl-Mozilla-CA-20200520-6.el9.noarc 210 kB/s |  14 kB     00:00    
(130/206): perl-Pod-Simple-3.42-4.el9.noarch.rp 2.3 MB/s | 229 kB     00:00    
(131/206): perl-Term-Cap-1.17-460.el9.noarch.rp 351 kB/s |  24 kB     00:00    
(132/206): perl-Time-Local-1.300-7.el9.noarch.r 530 kB/s |  37 kB     00:00    
(133/206): rust-srpm-macros-17-4.el9.noarch.rpm 161 kB/s |  11 kB     00:00    
(134/206): perl-Pod-Escapes-1.07-460.el9.noarch 304 kB/s |  22 kB     00:00    
(135/206): perl-Storable-3.21-460.el9.x86_64.rp 871 kB/s |  98 kB     00:00    
(136/206): perl-podlators-4.14-460.el9.noarch.r 1.5 MB/s | 118 kB     00:00    
(137/206): dwz-0.14-3.el9.x86_64.rpm            1.8 MB/s | 130 kB     00:00    
(138/206): perl-Exporter-5.74-461.el9.noarch.rp 402 kB/s |  34 kB     00:00    
(139/206): perl-Getopt-Long-2.52-4.el9.noarch.r 879 kB/s |  64 kB     00:00    
(140/206): perl-File-Temp-0.231.100-4.el9.noarc 434 kB/s |  63 kB     00:00    
(141/206): perl-MIME-Base64-3.16-4.el9.x86_64.r 429 kB/s |  34 kB     00:00    
(142/206): perl-Text-Tabs+Wrap-2013.0523-460.el 371 kB/s |  25 kB     00:00    
(143/206): perl-parent-0.238-460.el9.noarch.rpm 228 kB/s |  16 kB     00:00    
(144/206): perl-srpm-macros-1-41.el9.noarch.rpm 137 kB/s | 9.4 kB     00:00    
(145/206): efi-srpm-macros-6-2.el9_0.noarch.rpm 330 kB/s |  24 kB     00:00    
(146/206): openblas-srpm-macros-2-11.el9.noarch 129 kB/s | 8.6 kB     00:00    
(147/206): perl-Digest-1.19-4.el9.noarch.rpm    399 kB/s |  29 kB     00:00    
(148/206): perl-File-Path-2.18-4.el9.noarch.rpm 281 kB/s |  38 kB     00:00    
(149/206): perl-IO-Socket-IP-0.41-5.el9.noarch. 327 kB/s |  45 kB     00:00    
(150/206): perl-Pod-Usage-2.01-4.el9.noarch.rpm 644 kB/s |  43 kB     00:00    
(151/206): perl-Scalar-List-Utils-1.56-461.el9. 1.1 MB/s |  77 kB     00:00    
(152/206): perl-Socket-2.031-4.el9.x86_64.rpm   866 kB/s |  58 kB     00:00    
(153/206): perl-Term-ANSIColor-5.01-461.el9.noa 529 kB/s |  51 kB     00:00    
(154/206): perl-Text-ParseWords-3.30-460.el9.no 172 kB/s |  18 kB     00:00    
(155/206): perl-URI-5.09-3.el9.noarch.rpm       1.5 MB/s | 125 kB     00:00    
(156/206): perl-constant-1.33-461.el9.noarch.rp 350 kB/s |  25 kB     00:00    
(157/206): fonts-srpm-macros-2.0.5-7.el9.1.noar 437 kB/s |  29 kB     00:00    
(158/206): ocaml-srpm-macros-6-6.el9.noarch.rpm 132 kB/s | 9.1 kB     00:00    
(159/206): patch-2.7.6-16.el9.x86_64.rpm        1.4 MB/s | 130 kB     00:00    
(160/206): perl-Pod-Perldoc-3.28.01-461.el9.noa 822 kB/s |  92 kB     00:00    
(161/206): perl-libnet-3.13-4.el9.noarch.rpm    1.4 MB/s | 134 kB     00:00    
(162/206): perl-Carp-1.50-460.el9.noarch.rpm    471 kB/s |  31 kB     00:00    
(163/206): perl-PathTools-3.78-461.el9.x86_64.r 1.3 MB/s |  92 kB     00:00    
(164/206): perl-Net-SSLeay-1.92-2.el9.x86_64.rp 4.9 MB/s | 392 kB     00:00    
(165/206): kernel-srpm-macros-1.0-13.el9.noarch 236 kB/s |  17 kB     00:00    
(166/206): qt5-srpm-macros-5.15.9-1.el9.noarch.  81 kB/s | 9.1 kB     00:00    
(167/206): perl-AutoLoader-5.74-481.el9.noarch. 317 kB/s |  21 kB     00:00    
(168/206): perl-SelectSaver-1.02-481.el9.noarch 175 kB/s |  12 kB     00:00    
(169/206): perl-if-0.60.800-481.el9.noarch.rpm  209 kB/s |  14 kB     00:00    
(170/206): perl-overloading-0.02-481.el9.noarch  99 kB/s |  13 kB     00:00    
(171/206): python-srpm-macros-3.9-53.el9.noarch 147 kB/s |  19 kB     00:00    
(172/206): redhat-rpm-config-207-1.el9.noarch.r 547 kB/s |  76 kB     00:00    
(173/206): gdb-minimal-10.2-13.el9.x86_64.rpm    20 MB/s | 3.5 MB     00:00    
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(175/206): perl-B-1.80-481.el9.x86_64.rpm       2.6 MB/s | 184 kB     00:00    
(176/206): perl-Class-Struct-0.66-481.el9.noarc 312 kB/s |  22 kB     00:00    
(177/206): perl-Errno-1.30-481.el9.x86_64.rpm   209 kB/s |  15 kB     00:00    
(178/206): perl-File-stat-1.09-481.el9.noarch.r 257 kB/s |  17 kB     00:00    
(179/206): perl-File-Basename-2.85-481.el9.noar 189 kB/s |  17 kB     00:00    
(180/206): perl-FileHandle-2.03-481.el9.noarch. 233 kB/s |  16 kB     00:00    
(181/206): perl-Getopt-Std-1.12-481.el9.noarch. 171 kB/s |  16 kB     00:00    
(182/206): perl-HTTP-Tiny-0.076-462.el9.noarch. 819 kB/s |  57 kB     00:00    
(183/206): perl-IO-1.43-481.el9.x86_64.rpm      1.3 MB/s |  92 kB     00:00    
(184/206): perl-IPC-Open3-1.21-481.el9.noarch.r 345 kB/s |  24 kB     00:00    
(185/206): perl-POSIX-1.94-481.el9.x86_64.rpm   1.3 MB/s |  98 kB     00:00    
(186/206): perl-Symbol-1.08-481.el9.noarch.rpm  186 kB/s |  14 kB     00:00    
(187/206): perl-base-2.27-481.el9.noarch.rpm    221 kB/s |  16 kB     00:00    
(188/206): perl-interpreter-5.32.1-481.el9.x86_ 851 kB/s |  73 kB     00:00    
(189/206): perl-libs-5.32.1-481.el9.x86_64.rpm   18 MB/s | 2.2 MB     00:00    
(190/206): perl-mro-1.23-481.el9.x86_64.rpm     419 kB/s |  29 kB     00:00    
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(198/206): ansible-srpm-macros-1-12.el9.noarch.  68 kB/s |  21 kB     00:00    
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(203/206): qt6-srpm-macros-6.6.2-1.el9.noarch.r 249 kB/s | 8.7 kB     00:00    
(204/206): rpmautospec-rpm-macros-0.6.3-1.el9.n 298 kB/s | 9.9 kB     00:00    
(205/206): rust-srpm-macros-epel-26.3-1.el9.noa 292 kB/s |  10 kB     00:00    
(206/206): util-linux-core-2.37.4-18.el9.x86_64  67 kB/s | 469 kB     00:07    
--------------------------------------------------------------------------------
Total                                           5.5 MB/s |  68 MB     00:12     
Red Hat Enterprise Linux - BaseOS               3.5 MB/s | 3.6 kB     00:00    
Importing GPG key 0xFD431D51:
 Userid     : "Red Hat, Inc. (release key 2) <security@redhat.com>"
 Fingerprint: 567E 347A D004 4ADE 55BA 8A5F 199E 2F91 FD43 1D51
 From       : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat9-release
Key imported successfully
Importing GPG key 0x5A6340B3:
 Userid     : "Red Hat, Inc. (auxiliary key 3) <security@redhat.com>"
 Fingerprint: 7E46 2425 8C40 6535 D56D 6F13 5054 E4A4 5A63 40B3
 From       : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat9-release
Key imported successfully
Extra Packages for Enterprise Linux 9 - x86_64  1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0x3228467C:
 Userid     : "Fedora (epel9) <epel@fedoraproject.org>"
 Fingerprint: FF8A D134 4597 106E CE81 3B91 8A38 72BF 3228 467C
 From       : /usr/share/distribution-gpg-keys/epel/RPM-GPG-KEY-EPEL-9
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.16-2.el9.x86_64                           1/1 
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warning: /etc/hosts created as /etc/hosts.rpmnew

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  Running scriptlet: which-2.21-29.el9.x86_64                           206/206 
  Verifying        : basesystem-11-13.el9.noarch                          1/206 
  Verifying        : bzip2-1.0.8-8.el9.x86_64                             2/206 
  Verifying        : bzip2-libs-1.0.8-8.el9.x86_64                        3/206 
  Verifying        : cpio-2.13-16.el9.x86_64                              4/206 
  Verifying        : cracklib-2.9.6-27.el9.x86_64                         5/206 
  Verifying        : ed-1.14.2-12.el9.x86_64                              6/206 
  Verifying        : filesystem-3.16-2.el9.x86_64                         7/206 
  Verifying        : grep-3.6-5.el9.x86_64                                8/206 
  Verifying        : groff-base-1.22.4-10.el9.x86_64                      9/206 
  Verifying        : info-6.7-15.el9.x86_64                              10/206 
  Verifying        : libattr-2.5.1-3.el9.x86_64                          11/206 
  Verifying        : libbrotli-1.0.9-6.el9.x86_64                        12/206 
  Verifying        : libcap-ng-0.8.2-7.el9.x86_64                        13/206 
  Verifying        : libdb-5.3.28-53.el9.x86_64                          14/206 
  Verifying        : libevent-2.1.12-6.el9.x86_64                        15/206 
  Verifying        : libgpg-error-1.42-5.el9.x86_64                      16/206 
  Verifying        : libidn2-2.3.0-7.el9.x86_64                          17/206 
  Verifying        : libpsl-0.21.1-5.el9.x86_64                          18/206 
  Verifying        : libpwquality-1.4.4-8.el9.x86_64                     19/206 
  Verifying        : libsigsegv-2.13-4.el9.x86_64                        20/206 
  Verifying        : libunistring-0.9.10-15.el9.x86_64                   21/206 
  Verifying        : libutempter-1.2.1-6.el9.x86_64                      22/206 
  Verifying        : libverto-0.3.2-3.el9.x86_64                         23/206 
  Verifying        : libxcrypt-4.4.18-3.el9.x86_64                       24/206 
  Verifying        : libzstd-1.5.1-2.el9.x86_64                          25/206 
  Verifying        : lz4-libs-1.9.3-5.el9.x86_64                         26/206 
  Verifying        : mpfr-4.1.0-7.el9.x86_64                             27/206 
  Verifying        : pcre-8.44-3.el9.3.x86_64                            28/206 
  Verifying        : popt-1.18-8.el9.x86_64                              29/206 
  Verifying        : publicsuffix-list-dafsa-20210518-3.el9.noarch       30/206 
  Verifying        : readline-8.1-4.el9.x86_64                           31/206 
  Verifying        : sed-4.8-9.el9.x86_64                                32/206 
  Verifying        : unzip-6.0-56.el9.x86_64                             33/206 
  Verifying        : cracklib-dicts-2.9.6-27.el9.x86_64                  34/206 
  Verifying        : diffutils-3.7-12.el9.x86_64                         35/206 
  Verifying        : gawk-5.1.0-6.el9.x86_64                             36/206 
  Verifying        : gdbm-libs-1:1.19-4.el9.x86_64                       37/206 
  Verifying        : xz-5.2.5-8.el9_0.x86_64                             38/206 
  Verifying        : xz-libs-5.2.5-8.el9_0.x86_64                        39/206 
  Verifying        : zstd-1.5.1-2.el9.x86_64                             40/206 
  Verifying        : cyrus-sasl-lib-2.1.27-21.el9.x86_64                 41/206 
  Verifying        : gzip-1.12-1.el9.x86_64                              42/206 
  Verifying        : libtasn1-4.16.0-8.el9_1.x86_64                      43/206 
  Verifying        : tar-2:1.34-6.el9_1.x86_64                           44/206 
  Verifying        : ca-certificates-2023.2.60_v7.0.306-90.1.el9_2.no    45/206 
  Verifying        : keyutils-libs-1.6.3-1.el9.x86_64                    46/206 
  Verifying        : libarchive-3.5.3-4.el9.x86_64                       47/206 
  Verifying        : libcap-2.48-9.el9_2.x86_64                          48/206 
  Verifying        : libeconf-0.4.1-3.el9_2.x86_64                       49/206 
  Verifying        : libgcrypt-1.10.0-10.el9_2.x86_64                    50/206 
  Verifying        : libpkgconf-1.7.3-10.el9.x86_64                      51/206 
  Verifying        : pkgconf-1.7.3-10.el9.x86_64                         52/206 
  Verifying        : pkgconf-m4-1.7.3-10.el9.noarch                      53/206 
  Verifying        : pkgconf-pkg-config-1.7.3-10.el9.x86_64              54/206 
  Verifying        : zip-3.0-35.el9.x86_64                               55/206 
  Verifying        : alternatives-1.24-1.el9.x86_64                      56/206 
  Verifying        : findutils-1:4.8.0-6.el9.x86_64                      57/206 
  Verifying        : gmp-1:6.2.0-13.el9.x86_64                           58/206 
  Verifying        : krb5-libs-1.21.1-1.el9.x86_64                       59/206 
  Verifying        : libffi-3.4.2-8.el9.x86_64                           60/206 
  Verifying        : lua-libs-5.4.4-4.el9.x86_64                         61/206 
  Verifying        : ncurses-6.2-10.20210508.el9.x86_64                  62/206 
  Verifying        : ncurses-base-6.2-10.20210508.el9.noarch             63/206 
  Verifying        : ncurses-libs-6.2-10.20210508.el9.x86_64             64/206 
  Verifying        : shadow-utils-2:4.9-8.el9.x86_64                     65/206 
  Verifying        : which-2.21-29.el9.x86_64                            66/206 
  Verifying        : zlib-1.2.11-40.el9.x86_64                           67/206 
  Verifying        : audit-libs-3.1.2-2.el9.x86_64                       68/206 
  Verifying        : bash-5.1.8-9.el9.x86_64                             69/206 
  Verifying        : binutils-2.35.2-43.el9.x86_64                       70/206 
  Verifying        : binutils-gold-2.35.2-43.el9.x86_64                  71/206 
  Verifying        : coreutils-8.32-35.el9.x86_64                        72/206 
  Verifying        : coreutils-common-8.32-35.el9.x86_64                 73/206 
  Verifying        : curl-7.76.1-29.el9_4.x86_64                         74/206 
  Verifying        : elfutils-0.190-2.el9.x86_64                         75/206 
  Verifying        : elfutils-default-yama-scope-0.190-2.el9.noarch      76/206 
  Verifying        : elfutils-libs-0.190-2.el9.x86_64                    77/206 
  Verifying        : file-5.39-16.el9.x86_64                             78/206 
  Verifying        : file-libs-5.39-16.el9.x86_64                        79/206 
  Verifying        : libacl-2.3.1-4.el9.x86_64                           80/206 
  Verifying        : libblkid-2.37.4-18.el9.x86_64                       81/206 
  Verifying        : libfdisk-2.37.4-18.el9.x86_64                       82/206 
  Verifying        : libgcc-11.4.1-3.el9.x86_64                          83/206 
  Verifying        : libgomp-11.4.1-3.el9.x86_64                         84/206 
  Verifying        : libmount-2.37.4-18.el9.x86_64                       85/206 
  Verifying        : libselinux-3.6-1.el9.x86_64                         86/206 
  Verifying        : libsemanage-3.6-1.el9.x86_64                        87/206 
  Verifying        : libsepol-3.6-1.el9.x86_64                           88/206 
  Verifying        : libsmartcols-2.37.4-18.el9.x86_64                   89/206 
  Verifying        : libstdc++-11.4.1-3.el9.x86_64                       90/206 
  Verifying        : libuuid-2.37.4-18.el9.x86_64                        91/206 
  Verifying        : openldap-2.6.6-3.el9.x86_64                         92/206 
  Verifying        : openssl-1:3.0.7-27.el9.x86_64                       93/206 
  Verifying        : openssl-fips-provider-3.0.7-2.el9.x86_64            94/206 
  Verifying        : openssl-libs-1:3.0.7-27.el9.x86_64                  95/206 
  Verifying        : p11-kit-0.25.3-2.el9.x86_64                         96/206 
  Verifying        : p11-kit-trust-0.25.3-2.el9.x86_64                   97/206 
  Verifying        : pam-1.5.1-19.el9.x86_64                             98/206 
  Verifying        : pcre2-10.40-5.el9.x86_64                            99/206 
  Verifying        : rpm-4.16.1.3-29.el9.x86_64                         100/206 
  Verifying        : rpm-build-libs-4.16.1.3-29.el9.x86_64              101/206 
  Verifying        : rpm-libs-4.16.1.3-29.el9.x86_64                    102/206 
  Verifying        : setup-2.13.7-10.el9.noarch                         103/206 
  Verifying        : sqlite-libs-3.34.1-7.el9_3.x86_64                  104/206 
  Verifying        : systemd-libs-252-32.el9_4.x86_64                   105/206 
  Verifying        : tzdata-2024a-1.el9.noarch                          106/206 
  Verifying        : util-linux-2.37.4-18.el9.x86_64                    107/206 
  Verifying        : util-linux-core-2.37.4-18.el9.x86_64               108/206 
  Verifying        : crypto-policies-20240202-1.git283706d.el9.noarch   109/206 
  Verifying        : elfutils-debuginfod-client-0.190-2.el9.x86_64      110/206 
  Verifying        : elfutils-libelf-0.190-2.el9.x86_64                 111/206 
  Verifying        : libcom_err-1.46.5-5.el9.x86_64                     112/206 
  Verifying        : libcurl-7.76.1-29.el9_4.x86_64                     113/206 
  Verifying        : libssh-0.10.4-13.el9.x86_64                        114/206 
  Verifying        : libssh-config-0.10.4-13.el9.noarch                 115/206 
  Verifying        : pcre2-syntax-10.40-5.el9.noarch                    116/206 
  Verifying        : redhat-release-9.4-0.4.el9.x86_64                  117/206 
  Verifying        : libxml2-2.9.13-6.el9_4.x86_64                      118/206 
  Verifying        : glibc-2.34-100.el9_4.2.x86_64                      119/206 
  Verifying        : glibc-common-2.34-100.el9_4.2.x86_64               120/206 
  Verifying        : glibc-gconv-extra-2.34-100.el9_4.2.x86_64          121/206 
  Verifying        : glibc-minimal-langpack-2.34-100.el9_4.2.x86_64     122/206 
  Verifying        : libnghttp2-1.43.0-5.el9_4.3.x86_64                 123/206 
  Verifying        : ghc-srpm-macros-1.5.0-6.el9.noarch                 124/206 
  Verifying        : lua-srpm-macros-1-6.el9.noarch                     125/206 
  Verifying        : perl-Data-Dumper-2.174-462.el9.x86_64              126/206 
  Verifying        : perl-Digest-MD5-2.58-4.el9.x86_64                  127/206 
  Verifying        : perl-Encode-4:3.08-462.el9.x86_64                  128/206 
  Verifying        : perl-IO-Socket-SSL-2.073-1.el9.noarch              129/206 
  Verifying        : perl-Mozilla-CA-20200520-6.el9.noarch              130/206 
  Verifying        : perl-Pod-Simple-1:3.42-4.el9.noarch                131/206 
  Verifying        : perl-Term-Cap-1.17-460.el9.noarch                  132/206 
  Verifying        : perl-Time-Local-2:1.300-7.el9.noarch               133/206 
  Verifying        : rust-srpm-macros-17-4.el9.noarch                   134/206 
  Verifying        : perl-Pod-Escapes-1:1.07-460.el9.noarch             135/206 
  Verifying        : perl-Storable-1:3.21-460.el9.x86_64                136/206 
  Verifying        : perl-podlators-1:4.14-460.el9.noarch               137/206 
  Verifying        : dwz-0.14-3.el9.x86_64                              138/206 
  Verifying        : perl-Exporter-5.74-461.el9.noarch                  139/206 
  Verifying        : perl-File-Temp-1:0.231.100-4.el9.noarch            140/206 
  Verifying        : perl-Getopt-Long-1:2.52-4.el9.noarch               141/206 
  Verifying        : perl-MIME-Base64-3.16-4.el9.x86_64                 142/206 
  Verifying        : perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch       143/206 
  Verifying        : perl-parent-1:0.238-460.el9.noarch                 144/206 
  Verifying        : perl-srpm-macros-1-41.el9.noarch                   145/206 
  Verifying        : efi-srpm-macros-6-2.el9_0.noarch                   146/206 
  Verifying        : openblas-srpm-macros-2-11.el9.noarch               147/206 
  Verifying        : perl-Digest-1.19-4.el9.noarch                      148/206 
  Verifying        : perl-File-Path-2.18-4.el9.noarch                   149/206 
  Verifying        : perl-IO-Socket-IP-0.41-5.el9.noarch                150/206 
  Verifying        : perl-Pod-Usage-4:2.01-4.el9.noarch                 151/206 
  Verifying        : perl-Scalar-List-Utils-4:1.56-461.el9.x86_64       152/206 
  Verifying        : perl-Socket-4:2.031-4.el9.x86_64                   153/206 
  Verifying        : perl-Term-ANSIColor-5.01-461.el9.noarch            154/206 
  Verifying        : perl-Text-ParseWords-3.30-460.el9.noarch           155/206 
  Verifying        : perl-URI-5.09-3.el9.noarch                         156/206 
  Verifying        : perl-constant-1.33-461.el9.noarch                  157/206 
  Verifying        : fonts-srpm-macros-1:2.0.5-7.el9.1.noarch           158/206 
  Verifying        : ocaml-srpm-macros-6-6.el9.noarch                   159/206 
  Verifying        : patch-2.7.6-16.el9.x86_64                          160/206 
  Verifying        : perl-Pod-Perldoc-3.28.01-461.el9.noarch            161/206 
  Verifying        : perl-libnet-3.13-4.el9.noarch                      162/206 
  Verifying        : perl-Carp-1.50-460.el9.noarch                      163/206 
  Verifying        : perl-PathTools-3.78-461.el9.x86_64                 164/206 
  Verifying        : perl-Net-SSLeay-1.92-2.el9.x86_64                  165/206 
  Verifying        : kernel-srpm-macros-1.0-13.el9.noarch               166/206 
  Verifying        : qt5-srpm-macros-5.15.9-1.el9.noarch                167/206 
  Verifying        : perl-AutoLoader-5.74-481.el9.noarch                168/206 
  Verifying        : perl-SelectSaver-1.02-481.el9.noarch               169/206 
  Verifying        : perl-if-0.60.800-481.el9.noarch                    170/206 
  Verifying        : perl-overloading-0.02-481.el9.noarch               171/206 
  Verifying        : python-srpm-macros-3.9-53.el9.noarch               172/206 
  Verifying        : redhat-rpm-config-207-1.el9.noarch                 173/206 
  Verifying        : gdb-minimal-10.2-13.el9.x86_64                     174/206 
  Verifying        : go-srpm-macros-3.2.0-3.el9.noarch                  175/206 
  Verifying        : perl-B-1.80-481.el9.x86_64                         176/206 
  Verifying        : perl-Class-Struct-0.66-481.el9.noarch              177/206 
  Verifying        : perl-Errno-1.30-481.el9.x86_64                     178/206 
  Verifying        : perl-File-Basename-2.85-481.el9.noarch             179/206 
  Verifying        : perl-File-stat-1.09-481.el9.noarch                 180/206 
  Verifying        : perl-FileHandle-2.03-481.el9.noarch                181/206 
  Verifying        : perl-Getopt-Std-1.12-481.el9.noarch                182/206 
  Verifying        : perl-HTTP-Tiny-0.076-462.el9.noarch                183/206 
  Verifying        : perl-IO-1.43-481.el9.x86_64                        184/206 
  Verifying        : perl-IPC-Open3-1.21-481.el9.noarch                 185/206 
  Verifying        : perl-POSIX-1.94-481.el9.x86_64                     186/206 
  Verifying        : perl-Symbol-1.08-481.el9.noarch                    187/206 
  Verifying        : perl-base-2.27-481.el9.noarch                      188/206 
  Verifying        : perl-interpreter-4:5.32.1-481.el9.x86_64           189/206 
  Verifying        : perl-libs-4:5.32.1-481.el9.x86_64                  190/206 
  Verifying        : perl-mro-1.23-481.el9.x86_64                       191/206 
  Verifying        : perl-overload-1.31-481.el9.noarch                  192/206 
  Verifying        : perl-vars-1.05-481.el9.noarch                      193/206 
  Verifying        : pyproject-srpm-macros-1.12.0-1.el9.noarch          194/206 
  Verifying        : debugedit-5.0-5.el9.x86_64                         195/206 
  Verifying        : perl-Fcntl-1.13-481.el9.x86_64                     196/206 
  Verifying        : perl-subs-1.03-481.el9.noarch                      197/206 
  Verifying        : rpm-build-4.16.1.3-29.el9.x86_64                   198/206 
  Verifying        : ansible-srpm-macros-1-12.el9.noarch                199/206 
  Verifying        : epel-rpm-macros-9-14.el9.noarch                    200/206 
  Verifying        : forge-srpm-macros-0.3.1-1.el9.noarch               201/206 
  Verifying        : fpc-srpm-macros-1.3-7.el9.noarch                   202/206 
  Verifying        : go-srpm-macros-epel-3.3.0.5-1.el9.noarch           203/206 
  Verifying        : qt6-srpm-macros-6.6.2-1.el9.noarch                 204/206 
  Verifying        : rpmautospec-rpm-macros-0.6.3-1.el9.noarch          205/206 
  Verifying        : rust-srpm-macros-epel-26.3-1.el9.noarch            206/206 
Installed products updated.

Installed:
  alternatives-1.24-1.el9.x86_64                                                
  ansible-srpm-macros-1-12.el9.noarch                                           
  audit-libs-3.1.2-2.el9.x86_64                                                 
  basesystem-11-13.el9.noarch                                                   
  bash-5.1.8-9.el9.x86_64                                                       
  binutils-2.35.2-43.el9.x86_64                                                 
  binutils-gold-2.35.2-43.el9.x86_64                                            
  bzip2-1.0.8-8.el9.x86_64                                                      
  bzip2-libs-1.0.8-8.el9.x86_64                                                 
  ca-certificates-2023.2.60_v7.0.306-90.1.el9_2.noarch                          
  coreutils-8.32-35.el9.x86_64                                                  
  coreutils-common-8.32-35.el9.x86_64                                           
  cpio-2.13-16.el9.x86_64                                                       
  cracklib-2.9.6-27.el9.x86_64                                                  
  cracklib-dicts-2.9.6-27.el9.x86_64                                            
  crypto-policies-20240202-1.git283706d.el9.noarch                              
  curl-7.76.1-29.el9_4.x86_64                                                   
  cyrus-sasl-lib-2.1.27-21.el9.x86_64                                           
  debugedit-5.0-5.el9.x86_64                                                    
  diffutils-3.7-12.el9.x86_64                                                   
  dwz-0.14-3.el9.x86_64                                                         
  ed-1.14.2-12.el9.x86_64                                                       
  efi-srpm-macros-6-2.el9_0.noarch                                              
  elfutils-0.190-2.el9.x86_64                                                   
  elfutils-debuginfod-client-0.190-2.el9.x86_64                                 
  elfutils-default-yama-scope-0.190-2.el9.noarch                                
  elfutils-libelf-0.190-2.el9.x86_64                                            
  elfutils-libs-0.190-2.el9.x86_64                                              
  epel-rpm-macros-9-14.el9.noarch                                               
  file-5.39-16.el9.x86_64                                                       
  file-libs-5.39-16.el9.x86_64                                                  
  filesystem-3.16-2.el9.x86_64                                                  
  findutils-1:4.8.0-6.el9.x86_64                                                
  fonts-srpm-macros-1:2.0.5-7.el9.1.noarch                                      
  forge-srpm-macros-0.3.1-1.el9.noarch                                          
  fpc-srpm-macros-1.3-7.el9.noarch                                              
  gawk-5.1.0-6.el9.x86_64                                                       
  gdb-minimal-10.2-13.el9.x86_64                                                
  gdbm-libs-1:1.19-4.el9.x86_64                                                 
  ghc-srpm-macros-1.5.0-6.el9.noarch                                            
  glibc-2.34-100.el9_4.2.x86_64                                                 
  glibc-common-2.34-100.el9_4.2.x86_64                                          
  glibc-gconv-extra-2.34-100.el9_4.2.x86_64                                     
  glibc-minimal-langpack-2.34-100.el9_4.2.x86_64                                
  gmp-1:6.2.0-13.el9.x86_64                                                     
  go-srpm-macros-3.2.0-3.el9.noarch                                             
  go-srpm-macros-epel-3.3.0.5-1.el9.noarch                                      
  grep-3.6-5.el9.x86_64                                                         
  groff-base-1.22.4-10.el9.x86_64                                               
  gzip-1.12-1.el9.x86_64                                                        
  info-6.7-15.el9.x86_64                                                        
  kernel-srpm-macros-1.0-13.el9.noarch                                          
  keyutils-libs-1.6.3-1.el9.x86_64                                              
  krb5-libs-1.21.1-1.el9.x86_64                                                 
  libacl-2.3.1-4.el9.x86_64                                                     
  libarchive-3.5.3-4.el9.x86_64                                                 
  libattr-2.5.1-3.el9.x86_64                                                    
  libblkid-2.37.4-18.el9.x86_64                                                 
  libbrotli-1.0.9-6.el9.x86_64                                                  
  libcap-2.48-9.el9_2.x86_64                                                    
  libcap-ng-0.8.2-7.el9.x86_64                                                  
  libcom_err-1.46.5-5.el9.x86_64                                                
  libcurl-7.76.1-29.el9_4.x86_64                                                
  libdb-5.3.28-53.el9.x86_64                                                    
  libeconf-0.4.1-3.el9_2.x86_64                                                 
  libevent-2.1.12-6.el9.x86_64                                                  
  libfdisk-2.37.4-18.el9.x86_64                                                 
  libffi-3.4.2-8.el9.x86_64                                                     
  libgcc-11.4.1-3.el9.x86_64                                                    
  libgcrypt-1.10.0-10.el9_2.x86_64                                              
  libgomp-11.4.1-3.el9.x86_64                                                   
  libgpg-error-1.42-5.el9.x86_64                                                
  libidn2-2.3.0-7.el9.x86_64                                                    
  libmount-2.37.4-18.el9.x86_64                                                 
  libnghttp2-1.43.0-5.el9_4.3.x86_64                                            
  libpkgconf-1.7.3-10.el9.x86_64                                                
  libpsl-0.21.1-5.el9.x86_64                                                    
  libpwquality-1.4.4-8.el9.x86_64                                               
  libselinux-3.6-1.el9.x86_64                                                   
  libsemanage-3.6-1.el9.x86_64                                                  
  libsepol-3.6-1.el9.x86_64                                                     
  libsigsegv-2.13-4.el9.x86_64                                                  
  libsmartcols-2.37.4-18.el9.x86_64                                             
  libssh-0.10.4-13.el9.x86_64                                                   
  libssh-config-0.10.4-13.el9.noarch                                            
  libstdc++-11.4.1-3.el9.x86_64                                                 
  libtasn1-4.16.0-8.el9_1.x86_64                                                
  libunistring-0.9.10-15.el9.x86_64                                             
  libutempter-1.2.1-6.el9.x86_64                                                
  libuuid-2.37.4-18.el9.x86_64                                                  
  libverto-0.3.2-3.el9.x86_64                                                   
  libxcrypt-4.4.18-3.el9.x86_64                                                 
  libxml2-2.9.13-6.el9_4.x86_64                                                 
  libzstd-1.5.1-2.el9.x86_64                                                    
  lua-libs-5.4.4-4.el9.x86_64                                                   
  lua-srpm-macros-1-6.el9.noarch                                                
  lz4-libs-1.9.3-5.el9.x86_64                                                   
  mpfr-4.1.0-7.el9.x86_64                                                       
  ncurses-6.2-10.20210508.el9.x86_64                                            
  ncurses-base-6.2-10.20210508.el9.noarch                                       
  ncurses-libs-6.2-10.20210508.el9.x86_64                                       
  ocaml-srpm-macros-6-6.el9.noarch                                              
  openblas-srpm-macros-2-11.el9.noarch                                          
  openldap-2.6.6-3.el9.x86_64                                                   
  openssl-1:3.0.7-27.el9.x86_64                                                 
  openssl-fips-provider-3.0.7-2.el9.x86_64                                      
  openssl-libs-1:3.0.7-27.el9.x86_64                                            
  p11-kit-0.25.3-2.el9.x86_64                                                   
  p11-kit-trust-0.25.3-2.el9.x86_64                                             
  pam-1.5.1-19.el9.x86_64                                                       
  patch-2.7.6-16.el9.x86_64                                                     
  pcre-8.44-3.el9.3.x86_64                                                      
  pcre2-10.40-5.el9.x86_64                                                      
  pcre2-syntax-10.40-5.el9.noarch                                               
  perl-AutoLoader-5.74-481.el9.noarch                                           
  perl-B-1.80-481.el9.x86_64                                                    
  perl-Carp-1.50-460.el9.noarch                                                 
  perl-Class-Struct-0.66-481.el9.noarch                                         
  perl-Data-Dumper-2.174-462.el9.x86_64                                         
  perl-Digest-1.19-4.el9.noarch                                                 
  perl-Digest-MD5-2.58-4.el9.x86_64                                             
  perl-Encode-4:3.08-462.el9.x86_64                                             
  perl-Errno-1.30-481.el9.x86_64                                                
  perl-Exporter-5.74-461.el9.noarch                                             
  perl-Fcntl-1.13-481.el9.x86_64                                                
  perl-File-Basename-2.85-481.el9.noarch                                        
  perl-File-Path-2.18-4.el9.noarch                                              
  perl-File-Temp-1:0.231.100-4.el9.noarch                                       
  perl-File-stat-1.09-481.el9.noarch                                            
  perl-FileHandle-2.03-481.el9.noarch                                           
  perl-Getopt-Long-1:2.52-4.el9.noarch                                          
  perl-Getopt-Std-1.12-481.el9.noarch                                           
  perl-HTTP-Tiny-0.076-462.el9.noarch                                           
  perl-IO-1.43-481.el9.x86_64                                                   
  perl-IO-Socket-IP-0.41-5.el9.noarch                                           
  perl-IO-Socket-SSL-2.073-1.el9.noarch                                         
  perl-IPC-Open3-1.21-481.el9.noarch                                            
  perl-MIME-Base64-3.16-4.el9.x86_64                                            
  perl-Mozilla-CA-20200520-6.el9.noarch                                         
  perl-Net-SSLeay-1.92-2.el9.x86_64                                             
  perl-POSIX-1.94-481.el9.x86_64                                                
  perl-PathTools-3.78-461.el9.x86_64                                            
  perl-Pod-Escapes-1:1.07-460.el9.noarch                                        
  perl-Pod-Perldoc-3.28.01-461.el9.noarch                                       
  perl-Pod-Simple-1:3.42-4.el9.noarch                                           
  perl-Pod-Usage-4:2.01-4.el9.noarch                                            
  perl-Scalar-List-Utils-4:1.56-461.el9.x86_64                                  
  perl-SelectSaver-1.02-481.el9.noarch                                          
  perl-Socket-4:2.031-4.el9.x86_64                                              
  perl-Storable-1:3.21-460.el9.x86_64                                           
  perl-Symbol-1.08-481.el9.noarch                                               
  perl-Term-ANSIColor-5.01-461.el9.noarch                                       
  perl-Term-Cap-1.17-460.el9.noarch                                             
  perl-Text-ParseWords-3.30-460.el9.noarch                                      
  perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch                                  
  perl-Time-Local-2:1.300-7.el9.noarch                                          
  perl-URI-5.09-3.el9.noarch                                                    
  perl-base-2.27-481.el9.noarch                                                 
  perl-constant-1.33-461.el9.noarch                                             
  perl-if-0.60.800-481.el9.noarch                                               
  perl-interpreter-4:5.32.1-481.el9.x86_64                                      
  perl-libnet-3.13-4.el9.noarch                                                 
  perl-libs-4:5.32.1-481.el9.x86_64                                             
  perl-mro-1.23-481.el9.x86_64                                                  
  perl-overload-1.31-481.el9.noarch                                             
  perl-overloading-0.02-481.el9.noarch                                          
  perl-parent-1:0.238-460.el9.noarch                                            
  perl-podlators-1:4.14-460.el9.noarch                                          
  perl-srpm-macros-1-41.el9.noarch                                              
  perl-subs-1.03-481.el9.noarch                                                 
  perl-vars-1.05-481.el9.noarch                                                 
  pkgconf-1.7.3-10.el9.x86_64                                                   
  pkgconf-m4-1.7.3-10.el9.noarch                                                
  pkgconf-pkg-config-1.7.3-10.el9.x86_64                                        
  popt-1.18-8.el9.x86_64                                                        
  publicsuffix-list-dafsa-20210518-3.el9.noarch                                 
  pyproject-srpm-macros-1.12.0-1.el9.noarch                                     
  python-srpm-macros-3.9-53.el9.noarch                                          
  qt5-srpm-macros-5.15.9-1.el9.noarch                                           
  qt6-srpm-macros-6.6.2-1.el9.noarch                                            
  readline-8.1-4.el9.x86_64                                                     
  redhat-release-9.4-0.4.el9.x86_64                                             
  redhat-rpm-config-207-1.el9.noarch                                            
  rpm-4.16.1.3-29.el9.x86_64                                                    
  rpm-build-4.16.1.3-29.el9.x86_64                                              
  rpm-build-libs-4.16.1.3-29.el9.x86_64                                         
  rpm-libs-4.16.1.3-29.el9.x86_64                                               
  rpmautospec-rpm-macros-0.6.3-1.el9.noarch                                     
  rust-srpm-macros-17-4.el9.noarch                                              
  rust-srpm-macros-epel-26.3-1.el9.noarch                                       
  sed-4.8-9.el9.x86_64                                                          
  setup-2.13.7-10.el9.noarch                                                    
  shadow-utils-2:4.9-8.el9.x86_64                                               
  sqlite-libs-3.34.1-7.el9_3.x86_64                                             
  systemd-libs-252-32.el9_4.x86_64                                              
  tar-2:1.34-6.el9_1.x86_64                                                     
  tzdata-2024a-1.el9.noarch                                                     
  unzip-6.0-56.el9.x86_64                                                       
  util-linux-2.37.4-18.el9.x86_64                                               
  util-linux-core-2.37.4-18.el9.x86_64                                          
  which-2.21-29.el9.x86_64                                                      
  xz-5.2.5-8.el9_0.x86_64                                                       
  xz-libs-5.2.5-8.el9_0.x86_64                                                  
  zip-3.0-35.el9.x86_64                                                         
  zlib-1.2.11-40.el9.x86_64                                                     
  zstd-1.5.1-2.el9.x86_64                                                       

Complete!
Finish: installing minimal buildroot with dnf
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: alternatives-1.24-1.el9.x86_64
ansible-srpm-macros-1-12.el9.noarch
audit-libs-3.1.2-2.el9.x86_64
basesystem-11-13.el9.noarch
bash-5.1.8-9.el9.x86_64
binutils-2.35.2-43.el9.x86_64
binutils-gold-2.35.2-43.el9.x86_64
bzip2-1.0.8-8.el9.x86_64
bzip2-libs-1.0.8-8.el9.x86_64
ca-certificates-2023.2.60_v7.0.306-90.1.el9_2.noarch
coreutils-8.32-35.el9.x86_64
coreutils-common-8.32-35.el9.x86_64
cpio-2.13-16.el9.x86_64
cracklib-2.9.6-27.el9.x86_64
cracklib-dicts-2.9.6-27.el9.x86_64
crypto-policies-20240202-1.git283706d.el9.noarch
curl-7.76.1-29.el9_4.x86_64
cyrus-sasl-lib-2.1.27-21.el9.x86_64
debugedit-5.0-5.el9.x86_64
diffutils-3.7-12.el9.x86_64
dwz-0.14-3.el9.x86_64
ed-1.14.2-12.el9.x86_64
efi-srpm-macros-6-2.el9_0.noarch
elfutils-0.190-2.el9.x86_64
elfutils-debuginfod-client-0.190-2.el9.x86_64
elfutils-default-yama-scope-0.190-2.el9.noarch
elfutils-libelf-0.190-2.el9.x86_64
elfutils-libs-0.190-2.el9.x86_64
epel-rpm-macros-9-14.el9.noarch
file-5.39-16.el9.x86_64
file-libs-5.39-16.el9.x86_64
filesystem-3.16-2.el9.x86_64
findutils-4.8.0-6.el9.x86_64
fonts-srpm-macros-2.0.5-7.el9.1.noarch
forge-srpm-macros-0.3.1-1.el9.noarch
fpc-srpm-macros-1.3-7.el9.noarch
gawk-5.1.0-6.el9.x86_64
gdb-minimal-10.2-13.el9.x86_64
gdbm-libs-1.19-4.el9.x86_64
ghc-srpm-macros-1.5.0-6.el9.noarch
glibc-2.34-100.el9_4.2.x86_64
glibc-common-2.34-100.el9_4.2.x86_64
glibc-gconv-extra-2.34-100.el9_4.2.x86_64
glibc-minimal-langpack-2.34-100.el9_4.2.x86_64
gmp-6.2.0-13.el9.x86_64
go-srpm-macros-3.2.0-3.el9.noarch
go-srpm-macros-epel-3.3.0.5-1.el9.noarch
gpg-pubkey-3228467c-613798eb
gpg-pubkey-5a6340b3-6229229e
gpg-pubkey-fd431d51-4ae0493b
grep-3.6-5.el9.x86_64
groff-base-1.22.4-10.el9.x86_64
gzip-1.12-1.el9.x86_64
info-6.7-15.el9.x86_64
kernel-srpm-macros-1.0-13.el9.noarch
keyutils-libs-1.6.3-1.el9.x86_64
krb5-libs-1.21.1-1.el9.x86_64
libacl-2.3.1-4.el9.x86_64
libarchive-3.5.3-4.el9.x86_64
libattr-2.5.1-3.el9.x86_64
libblkid-2.37.4-18.el9.x86_64
libbrotli-1.0.9-6.el9.x86_64
libcap-2.48-9.el9_2.x86_64
libcap-ng-0.8.2-7.el9.x86_64
libcom_err-1.46.5-5.el9.x86_64
libcurl-7.76.1-29.el9_4.x86_64
libdb-5.3.28-53.el9.x86_64
libeconf-0.4.1-3.el9_2.x86_64
libevent-2.1.12-6.el9.x86_64
libfdisk-2.37.4-18.el9.x86_64
libffi-3.4.2-8.el9.x86_64
libgcc-11.4.1-3.el9.x86_64
libgcrypt-1.10.0-10.el9_2.x86_64
libgomp-11.4.1-3.el9.x86_64
libgpg-error-1.42-5.el9.x86_64
libidn2-2.3.0-7.el9.x86_64
libmount-2.37.4-18.el9.x86_64
libnghttp2-1.43.0-5.el9_4.3.x86_64
libpkgconf-1.7.3-10.el9.x86_64
libpsl-0.21.1-5.el9.x86_64
libpwquality-1.4.4-8.el9.x86_64
libselinux-3.6-1.el9.x86_64
libsemanage-3.6-1.el9.x86_64
libsepol-3.6-1.el9.x86_64
libsigsegv-2.13-4.el9.x86_64
libsmartcols-2.37.4-18.el9.x86_64
libssh-0.10.4-13.el9.x86_64
libssh-config-0.10.4-13.el9.noarch
libstdc++-11.4.1-3.el9.x86_64
libtasn1-4.16.0-8.el9_1.x86_64
libunistring-0.9.10-15.el9.x86_64
libutempter-1.2.1-6.el9.x86_64
libuuid-2.37.4-18.el9.x86_64
libverto-0.3.2-3.el9.x86_64
libxcrypt-4.4.18-3.el9.x86_64
libxml2-2.9.13-6.el9_4.x86_64
libzstd-1.5.1-2.el9.x86_64
lua-libs-5.4.4-4.el9.x86_64
lua-srpm-macros-1-6.el9.noarch
lz4-libs-1.9.3-5.el9.x86_64
mpfr-4.1.0-7.el9.x86_64
ncurses-6.2-10.20210508.el9.x86_64
ncurses-base-6.2-10.20210508.el9.noarch
ncurses-libs-6.2-10.20210508.el9.x86_64
ocaml-srpm-macros-6-6.el9.noarch
openblas-srpm-macros-2-11.el9.noarch
openldap-2.6.6-3.el9.x86_64
openssl-3.0.7-27.el9.x86_64
openssl-fips-provider-3.0.7-2.el9.x86_64
openssl-libs-3.0.7-27.el9.x86_64
p11-kit-0.25.3-2.el9.x86_64
p11-kit-trust-0.25.3-2.el9.x86_64
pam-1.5.1-19.el9.x86_64
patch-2.7.6-16.el9.x86_64
pcre-8.44-3.el9.3.x86_64
pcre2-10.40-5.el9.x86_64
pcre2-syntax-10.40-5.el9.noarch
perl-AutoLoader-5.74-481.el9.noarch
perl-B-1.80-481.el9.x86_64
perl-Carp-1.50-460.el9.noarch
perl-Class-Struct-0.66-481.el9.noarch
perl-Data-Dumper-2.174-462.el9.x86_64
perl-Digest-1.19-4.el9.noarch
perl-Digest-MD5-2.58-4.el9.x86_64
perl-Encode-3.08-462.el9.x86_64
perl-Errno-1.30-481.el9.x86_64
perl-Exporter-5.74-461.el9.noarch
perl-Fcntl-1.13-481.el9.x86_64
perl-File-Basename-2.85-481.el9.noarch
perl-File-Path-2.18-4.el9.noarch
perl-File-Temp-0.231.100-4.el9.noarch
perl-File-stat-1.09-481.el9.noarch
perl-FileHandle-2.03-481.el9.noarch
perl-Getopt-Long-2.52-4.el9.noarch
perl-Getopt-Std-1.12-481.el9.noarch
perl-HTTP-Tiny-0.076-462.el9.noarch
perl-IO-1.43-481.el9.x86_64
perl-IO-Socket-IP-0.41-5.el9.noarch
perl-IO-Socket-SSL-2.073-1.el9.noarch
perl-IPC-Open3-1.21-481.el9.noarch
perl-MIME-Base64-3.16-4.el9.x86_64
perl-Mozilla-CA-20200520-6.el9.noarch
perl-Net-SSLeay-1.92-2.el9.x86_64
perl-POSIX-1.94-481.el9.x86_64
perl-PathTools-3.78-461.el9.x86_64
perl-Pod-Escapes-1.07-460.el9.noarch
perl-Pod-Perldoc-3.28.01-461.el9.noarch
perl-Pod-Simple-3.42-4.el9.noarch
perl-Pod-Usage-2.01-4.el9.noarch
perl-Scalar-List-Utils-1.56-461.el9.x86_64
perl-SelectSaver-1.02-481.el9.noarch
perl-Socket-2.031-4.el9.x86_64
perl-Storable-3.21-460.el9.x86_64
perl-Symbol-1.08-481.el9.noarch
perl-Term-ANSIColor-5.01-461.el9.noarch
perl-Term-Cap-1.17-460.el9.noarch
perl-Text-ParseWords-3.30-460.el9.noarch
perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch
perl-Time-Local-1.300-7.el9.noarch
perl-URI-5.09-3.el9.noarch
perl-base-2.27-481.el9.noarch
perl-constant-1.33-461.el9.noarch
perl-if-0.60.800-481.el9.noarch
perl-interpreter-5.32.1-481.el9.x86_64
perl-libnet-3.13-4.el9.noarch
perl-libs-5.32.1-481.el9.x86_64
perl-mro-1.23-481.el9.x86_64
perl-overload-1.31-481.el9.noarch
perl-overloading-0.02-481.el9.noarch
perl-parent-0.238-460.el9.noarch
perl-podlators-4.14-460.el9.noarch
perl-srpm-macros-1-41.el9.noarch
perl-subs-1.03-481.el9.noarch
perl-vars-1.05-481.el9.noarch
pkgconf-1.7.3-10.el9.x86_64
pkgconf-m4-1.7.3-10.el9.noarch
pkgconf-pkg-config-1.7.3-10.el9.x86_64
popt-1.18-8.el9.x86_64
publicsuffix-list-dafsa-20210518-3.el9.noarch
pyproject-srpm-macros-1.12.0-1.el9.noarch
python-srpm-macros-3.9-53.el9.noarch
qt5-srpm-macros-5.15.9-1.el9.noarch
qt6-srpm-macros-6.6.2-1.el9.noarch
readline-8.1-4.el9.x86_64
redhat-release-9.4-0.4.el9.x86_64
redhat-rpm-config-207-1.el9.noarch
rpm-4.16.1.3-29.el9.x86_64
rpm-build-4.16.1.3-29.el9.x86_64
rpm-build-libs-4.16.1.3-29.el9.x86_64
rpm-libs-4.16.1.3-29.el9.x86_64
rpmautospec-rpm-macros-0.6.3-1.el9.noarch
rust-srpm-macros-17-4.el9.noarch
rust-srpm-macros-epel-26.3-1.el9.noarch
sed-4.8-9.el9.x86_64
setup-2.13.7-10.el9.noarch
shadow-utils-4.9-8.el9.x86_64
sqlite-libs-3.34.1-7.el9_3.x86_64
systemd-libs-252-32.el9_4.x86_64
tar-1.34-6.el9_1.x86_64
tzdata-2024a-1.el9.noarch
unzip-6.0-56.el9.x86_64
util-linux-2.37.4-18.el9.x86_64
util-linux-core-2.37.4-18.el9.x86_64
which-2.21-29.el9.x86_64
xz-5.2.5-8.el9_0.x86_64
xz-libs-5.2.5-8.el9_0.x86_64
zip-3.0-35.el9.x86_64
zlib-1.2.11-40.el9.x86_64
zstd-1.5.1-2.el9.x86_64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1717372800
Wrote: /builddir/build/SRPMS/bcftools-1.20-1.el9.src.rpm
Finish: rpmbuild -bs
cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/rhel+epel-9-x86_64-1717414005.411382/root/var/log’: No such file or directory
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/rhel+epel-9-x86_64-1717414005.411382/root/var/log/dnf.log
/var/lib/mock/rhel+epel-9-x86_64-1717414005.411382/root/var/log/dnf.librepo.log
/var/lib/mock/rhel+epel-9-x86_64-1717414005.411382/root/var/log/dnf.rpm.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-4tv0db3h/bcftools/bcftools.spec) Config(child) 0 minutes 54 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/bcftools-1.20-1.el9.src.rpm)  Config(rhel+epel-9-x86_64)
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-x86_64-1717414005.411382/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Buildroot is handled by package management from host and used with --installroot:
  rpm-4.19.1.1-1.fc39.x86_64
  rpm-sequoia-1.6.0-1.fc39.x86_64
  python3-dnf-4.19.2-1.fc39.noarch
  python3-dnf-plugins-core-4.6.0-1.fc39.noarch
  yum-4.19.2-1.fc39.noarch
  dnf5-5.1.17-1.fc39.x86_64
  dnf5-plugins-5.1.17-1.fc39.x86_64
Finish: chroot init
Start: build phase for bcftools-1.20-1.el9.src.rpm
Start: build setup for bcftools-1.20-1.el9.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1717372800
Wrote: /builddir/build/SRPMS/bcftools-1.20-1.el9.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Updating Subscription Management repositories.
Unable to read consumer identity

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Copr repository                                  26 kB/s | 1.8 kB     00:00    
Red Hat Enterprise Linux - BaseOS                18 kB/s | 4.1 kB     00:00    
Red Hat Enterprise Linux - AppStream             31 kB/s | 4.5 kB     00:00    
Red Hat Enterprise Linux - CodeReady Linux Buil  22 kB/s | 4.5 kB     00:00    
Extra Packages for Enterprise Linux 9 - x86_64  461 kB/s |  12 kB     00:00    
Package perl-File-Temp-1:0.231.100-4.el9.noarch is already installed.
Package perl-Getopt-Long-1:2.52-4.el9.noarch is already installed.
Package perl-interpreter-4:5.32.1-481.el9.x86_64 is already installed.
Dependencies resolved.
================================================================================
 Package                    Arch     Version                  Repository   Size
================================================================================
Installing:
 gcc                        x86_64   11.4.1-3.el9             appstream    32 M
 gsl-devel                  x86_64   2.6-7.el9                appstream   652 k
 htslib-devel               x86_64   1.20-1.el9               copr_base   104 k
 htslib-tools               x86_64   1.20-1.el9               copr_base   660 k
 make                       x86_64   1:4.3-8.el9              baseos      541 k
 perl-ExtUtils-Embed        noarch   1.35-481.el9             appstream    18 k
 perl-FindBin               noarch   1.51-481.el9             appstream    14 k
 zlib-devel                 x86_64   1.2.11-40.el9            appstream    47 k
Installing dependencies:
 annobin                    x86_64   12.31-2.el9              appstream   1.0 M
 autoconf                   noarch   2.69-38.el9              appstream   685 k
 automake                   noarch   1.16.2-8.el9             appstream   693 k
 cpp                        x86_64   11.4.1-3.el9             appstream    11 M
 emacs-filesystem           noarch   1:27.2-9.el9             appstream   9.6 k
 expat                      x86_64   2.5.0-2.el9_4            baseos      119 k
 gcc-plugin-annobin         x86_64   11.4.1-3.el9             appstream    49 k
 glibc-devel                x86_64   2.34-100.el9_4.2         appstream    42 k
 glibc-headers              x86_64   2.34-100.el9_4.2         appstream   548 k
 gsl                        x86_64   2.6-7.el9                appstream   1.1 M
 htslib                     x86_64   1.20-1.el9               copr_base   546 k
 kernel-headers             x86_64   5.14.0-427.18.1.el9_4    appstream   7.4 M
 libedit                    x86_64   3.1-38.20210216cvs.el9   baseos      107 k
 libmpc                     x86_64   1.2.1-4.el9              appstream    65 k
 libxcrypt-devel            x86_64   4.4.18-3.el9             appstream    32 k
 llvm-libs                  x86_64   17.0.6-5.el9             appstream    25 M
 m4                         x86_64   1.4.19-1.el9             appstream   304 k
 perl-AutoSplit             noarch   5.74-481.el9             appstream    22 k
 perl-Benchmark             noarch   1.23-481.el9             appstream    27 k
 perl-Devel-PPPort          x86_64   3.62-4.el9               appstream   216 k
 perl-DynaLoader            x86_64   1.47-481.el9             appstream    26 k
 perl-ExtUtils-Command      noarch   2:7.60-3.el9             appstream    16 k
 perl-ExtUtils-Constant     noarch   0.25-481.el9             appstream    49 k
 perl-ExtUtils-Install      noarch   2.20-4.el9               appstream    47 k
 perl-ExtUtils-MakeMaker    noarch   2:7.60-3.el9             appstream   304 k
 perl-ExtUtils-Manifest     noarch   1:1.73-4.el9             appstream    37 k
 perl-ExtUtils-ParseXS      noarch   1:3.40-460.el9           appstream   190 k
 perl-File-Compare          noarch   1.100.600-481.el9        appstream    14 k
 perl-File-Copy             noarch   2.34-481.el9             appstream    20 k
 perl-File-Find             noarch   1.37-481.el9             appstream    26 k
 perl-Test-Harness          noarch   1:3.42-461.el9           appstream   299 k
 perl-Thread-Queue          noarch   3.14-460.el9             appstream    24 k
 perl-devel                 x86_64   4:5.32.1-481.el9         appstream   680 k
 perl-lib                   x86_64   0.65-481.el9             appstream    15 k
 perl-locale                noarch   1.09-481.el9             appstream    14 k
 perl-threads               x86_64   1:2.25-460.el9           appstream    61 k
 perl-threads-shared        x86_64   1.61-460.el9             appstream    48 k
 perl-version               x86_64   7:0.99.28-4.el9          appstream    67 k
 python3                    x86_64   3.9.18-3.el9             baseos       29 k
 python3-libs               x86_64   3.9.18-3.el9             baseos      7.8 M
 python3-pip-wheel          noarch   21.2.3-8.el9             baseos      1.1 M
 python3-pyparsing          noarch   2.4.7-9.el9              baseos      154 k
 python3-setuptools-wheel   noarch   53.0.0-12.el9            baseos      470 k
 systemtap-sdt-devel        x86_64   5.0-4.el9                appstream    77 k

Transaction Summary
================================================================================
Install  52 Packages

Total download size: 94 M
Installed size: 287 M
Downloading Packages:
(1/52): htslib-devel-1.20-1.el9.x86_64.rpm      1.3 MB/s | 104 kB     00:00    
(2/52): htslib-tools-1.20-1.el9.x86_64.rpm      4.6 MB/s | 660 kB     00:00    
(3/52): htslib-1.20-1.el9.x86_64.rpm            2.8 MB/s | 546 kB     00:00    
(4/52): python3-setuptools-wheel-53.0.0-12.el9. 1.8 MB/s | 470 kB     00:00    
(5/52): expat-2.5.0-2.el9_4.x86_64.rpm          1.6 MB/s | 119 kB     00:00    
(6/52): make-4.3-8.el9.x86_64.rpm               5.6 MB/s | 541 kB     00:00    
(7/52): python3-3.9.18-3.el9.x86_64.rpm         434 kB/s |  29 kB     00:00    
(8/52): python3-libs-3.9.18-3.el9.x86_64.rpm     39 MB/s | 7.8 MB     00:00    
(9/52): python3-pip-wheel-21.2.3-8.el9.noarch.r  13 MB/s | 1.1 MB     00:00    
(10/52): perl-ExtUtils-Install-2.20-4.el9.noarc 661 kB/s |  47 kB     00:00    
(11/52): perl-version-0.99.28-4.el9.x86_64.rpm  618 kB/s |  67 kB     00:00    
(12/52): perl-ExtUtils-MakeMaker-7.60-3.el9.noa 4.2 MB/s | 304 kB     00:00    
(13/52): perl-ExtUtils-Manifest-1.73-4.el9.noar 162 kB/s |  37 kB     00:00    
(14/52): python3-pyparsing-2.4.7-9.el9.noarch.r 108 kB/s | 154 kB     00:01    
(15/52): libmpc-1.2.1-4.el9.x86_64.rpm          486 kB/s |  65 kB     00:00    
(16/52): perl-ExtUtils-ParseXS-3.40-460.el9.noa 2.2 MB/s | 190 kB     00:00    
(17/52): autoconf-2.69-38.el9.noarch.rpm        8.5 MB/s | 685 kB     00:00    
(18/52): gsl-2.6-7.el9.x86_64.rpm               8.2 MB/s | 1.1 MB     00:00    
(19/52): perl-Test-Harness-3.42-461.el9.noarch. 4.1 MB/s | 299 kB     00:00    
(20/52): perl-threads-2.25-460.el9.x86_64.rpm   800 kB/s |  61 kB     00:00    
(21/52): libxcrypt-devel-4.4.18-3.el9.x86_64.rp  68 kB/s |  32 kB     00:00    
(22/52): m4-1.4.19-1.el9.x86_64.rpm             2.8 MB/s | 304 kB     00:00    
(23/52): perl-ExtUtils-Command-7.60-3.el9.noarc 234 kB/s |  16 kB     00:00    
(24/52): perl-Thread-Queue-3.14-460.el9.noarch. 181 kB/s |  24 kB     00:00    
(25/52): perl-threads-shared-1.61-460.el9.x86_6 568 kB/s |  48 kB     00:00    
(26/52): gsl-devel-2.6-7.el9.x86_64.rpm         8.2 MB/s | 652 kB     00:00    
(27/52): emacs-filesystem-27.2-9.el9.noarch.rpm  79 kB/s | 9.6 kB     00:00    
(28/52): automake-1.16.2-8.el9.noarch.rpm       6.5 MB/s | 693 kB     00:00    
(29/52): zlib-devel-1.2.11-40.el9.x86_64.rpm    634 kB/s |  47 kB     00:00    
(30/52): gcc-plugin-annobin-11.4.1-3.el9.x86_64 575 kB/s |  49 kB     00:00    
(31/52): perl-Benchmark-1.23-481.el9.noarch.rpm 190 kB/s |  27 kB     00:00    
(32/52): libedit-3.1-38.20210216cvs.el9.x86_64.  37 kB/s | 107 kB     00:02    
(33/52): perl-FindBin-1.51-481.el9.noarch.rpm    91 kB/s |  14 kB     00:00    
(34/52): annobin-12.31-2.el9.x86_64.rpm         9.6 MB/s | 1.0 MB     00:00    
(35/52): cpp-11.4.1-3.el9.x86_64.rpm             33 MB/s |  11 MB     00:00    
(36/52): llvm-libs-17.0.6-5.el9.x86_64.rpm       57 MB/s |  25 MB     00:00    
(37/52): perl-AutoSplit-5.74-481.el9.noarch.rpm 318 kB/s |  22 kB     00:00    
(38/52): systemtap-sdt-devel-5.0-4.el9.x86_64.r  76 kB/s |  77 kB     00:01    
(39/52): perl-ExtUtils-Constant-0.25-481.el9.no 705 kB/s |  49 kB     00:00    
(40/52): perl-File-Compare-1.100.600-481.el9.no 161 kB/s |  14 kB     00:00    
(41/52): perl-File-Copy-2.34-481.el9.noarch.rpm 294 kB/s |  20 kB     00:00    
(42/52): perl-File-Find-1.37-481.el9.noarch.rpm 371 kB/s |  26 kB     00:00    
(43/52): perl-devel-5.32.1-481.el9.x86_64.rpm   8.6 MB/s | 680 kB     00:00    
(44/52): perl-lib-0.65-481.el9.x86_64.rpm       195 kB/s |  15 kB     00:00    
(45/52): perl-locale-1.09-481.el9.noarch.rpm    186 kB/s |  14 kB     00:00    
(46/52): gcc-11.4.1-3.el9.x86_64.rpm             66 MB/s |  32 MB     00:00    
(47/52): perl-DynaLoader-1.47-481.el9.x86_64.rp 223 kB/s |  26 kB     00:00    
(48/52): kernel-headers-5.14.0-427.18.1.el9_4.x  43 MB/s | 7.4 MB     00:00    
(49/52): glibc-devel-2.34-100.el9_4.2.x86_64.rp 581 kB/s |  42 kB     00:00    
(50/52): glibc-headers-2.34-100.el9_4.2.x86_64. 7.1 MB/s | 548 kB     00:00    
(51/52): perl-Devel-PPPort-3.62-4.el9.x86_64.rp  51 kB/s | 216 kB     00:04    
(52/52): perl-ExtUtils-Embed-1.35-481.el9.noarc 4.5 kB/s |  18 kB     00:04    
--------------------------------------------------------------------------------
Total                                            12 MB/s |  94 MB     00:08     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
  Installing       : perl-File-Find-1.37-481.el9.noarch                    1/52 
  Installing       : perl-File-Copy-2.34-481.el9.noarch                    2/52 
  Installing       : perl-File-Compare-1.100.600-481.el9.noarch            3/52 
  Installing       : perl-DynaLoader-1.47-481.el9.x86_64                   4/52 
  Installing       : perl-threads-1:2.25-460.el9.x86_64                    5/52 
  Installing       : perl-ExtUtils-ParseXS-1:3.40-460.el9.noarch           6/52 
  Installing       : libmpc-1.2.1-4.el9.x86_64                             7/52 
  Installing       : htslib-1.20-1.el9.x86_64                              8/52 
  Installing       : cpp-11.4.1-3.el9.x86_64                               9/52 
  Installing       : perl-threads-shared-1.61-460.el9.x86_64              10/52 
  Installing       : perl-Thread-Queue-3.14-460.el9.noarch                11/52 
  Installing       : perl-ExtUtils-Manifest-1:1.73-4.el9.noarch           12/52 
  Installing       : perl-ExtUtils-Command-2:7.60-3.el9.noarch            13/52 
  Installing       : glibc-headers-2.34-100.el9_4.2.x86_64                14/52 
  Installing       : kernel-headers-5.14.0-427.18.1.el9_4.x86_64          15/52 
  Installing       : glibc-devel-2.34-100.el9_4.2.x86_64                  16/52 
  Installing       : libxcrypt-devel-4.4.18-3.el9.x86_64                  17/52 
  Installing       : perl-locale-1.09-481.el9.noarch                      18/52 
  Installing       : perl-version-7:0.99.28-4.el9.x86_64                  19/52 
  Installing       : perl-lib-0.65-481.el9.x86_64                         20/52 
  Installing       : perl-ExtUtils-Constant-0.25-481.el9.noarch           21/52 
  Installing       : perl-AutoSplit-5.74-481.el9.noarch                   22/52 
  Installing       : perl-Benchmark-1.23-481.el9.noarch                   23/52 
  Installing       : perl-Test-Harness-1:3.42-461.el9.noarch              24/52 
  Installing       : emacs-filesystem-1:27.2-9.el9.noarch                 25/52 
  Installing       : perl-Devel-PPPort-3.62-4.el9.x86_64                  26/52 
  Installing       : m4-1.4.19-1.el9.x86_64                               27/52 
  Installing       : autoconf-2.69-38.el9.noarch                          28/52 
  Installing       : automake-1.16.2-8.el9.noarch                         29/52 
  Installing       : gsl-2.6-7.el9.x86_64                                 30/52 
  Installing       : python3-pip-wheel-21.2.3-8.el9.noarch                31/52 
  Installing       : make-1:4.3-8.el9.x86_64                              32/52 
  Installing       : gcc-11.4.1-3.el9.x86_64                              33/52 
  Running scriptlet: gcc-11.4.1-3.el9.x86_64                              33/52 
  Installing       : expat-2.5.0-2.el9_4.x86_64                           34/52 
  Installing       : libedit-3.1-38.20210216cvs.el9.x86_64                35/52 
  Installing       : llvm-libs-17.0.6-5.el9.x86_64                        36/52 
  Installing       : python3-setuptools-wheel-53.0.0-12.el9.noarch        37/52 
  Installing       : python3-3.9.18-3.el9.x86_64                          38/52 
  Installing       : python3-libs-3.9.18-3.el9.x86_64                     39/52 
  Installing       : python3-pyparsing-2.4.7-9.el9.noarch                 40/52 
  Installing       : systemtap-sdt-devel-5.0-4.el9.x86_64                 41/52 
  Installing       : perl-ExtUtils-Install-2.20-4.el9.noarch              42/52 
  Installing       : perl-devel-4:5.32.1-481.el9.x86_64                   43/52 
  Installing       : perl-ExtUtils-MakeMaker-2:7.60-3.el9.noarch          44/52 
  Installing       : perl-ExtUtils-Embed-1.35-481.el9.noarch              45/52 
  Installing       : annobin-12.31-2.el9.x86_64                           46/52 
  Running scriptlet: annobin-12.31-2.el9.x86_64                           46/52 
  Installing       : gcc-plugin-annobin-11.4.1-3.el9.x86_64               47/52 
  Running scriptlet: gcc-plugin-annobin-11.4.1-3.el9.x86_64               47/52 
  Installing       : gsl-devel-2.6-7.el9.x86_64                           48/52 
  Installing       : htslib-devel-1.20-1.el9.x86_64                       49/52 
  Installing       : htslib-tools-1.20-1.el9.x86_64                       50/52 
  Installing       : perl-FindBin-1.51-481.el9.noarch                     51/52 
  Installing       : zlib-devel-1.2.11-40.el9.x86_64                      52/52 
  Running scriptlet: zlib-devel-1.2.11-40.el9.x86_64                      52/52 
  Verifying        : htslib-1.20-1.el9.x86_64                              1/52 
  Verifying        : htslib-devel-1.20-1.el9.x86_64                        2/52 
  Verifying        : htslib-tools-1.20-1.el9.x86_64                        3/52 
  Verifying        : python3-pyparsing-2.4.7-9.el9.noarch                  4/52 
  Verifying        : python3-setuptools-wheel-53.0.0-12.el9.noarch         5/52 
  Verifying        : libedit-3.1-38.20210216cvs.el9.x86_64                 6/52 
  Verifying        : expat-2.5.0-2.el9_4.x86_64                            7/52 
  Verifying        : make-1:4.3-8.el9.x86_64                               8/52 
  Verifying        : python3-3.9.18-3.el9.x86_64                           9/52 
  Verifying        : python3-libs-3.9.18-3.el9.x86_64                     10/52 
  Verifying        : python3-pip-wheel-21.2.3-8.el9.noarch                11/52 
  Verifying        : perl-ExtUtils-Install-2.20-4.el9.noarch              12/52 
  Verifying        : perl-version-7:0.99.28-4.el9.x86_64                  13/52 
  Verifying        : perl-ExtUtils-MakeMaker-2:7.60-3.el9.noarch          14/52 
  Verifying        : perl-ExtUtils-Manifest-1:1.73-4.el9.noarch           15/52 
  Verifying        : libmpc-1.2.1-4.el9.x86_64                            16/52 
  Verifying        : libxcrypt-devel-4.4.18-3.el9.x86_64                  17/52 
  Verifying        : perl-ExtUtils-ParseXS-1:3.40-460.el9.noarch          18/52 
  Verifying        : autoconf-2.69-38.el9.noarch                          19/52 
  Verifying        : gsl-2.6-7.el9.x86_64                                 20/52 
  Verifying        : perl-Test-Harness-1:3.42-461.el9.noarch              21/52 
  Verifying        : perl-threads-1:2.25-460.el9.x86_64                   22/52 
  Verifying        : m4-1.4.19-1.el9.x86_64                               23/52 
  Verifying        : perl-Devel-PPPort-3.62-4.el9.x86_64                  24/52 
  Verifying        : perl-ExtUtils-Command-2:7.60-3.el9.noarch            25/52 
  Verifying        : perl-Thread-Queue-3.14-460.el9.noarch                26/52 
  Verifying        : perl-threads-shared-1.61-460.el9.x86_64              27/52 
  Verifying        : gsl-devel-2.6-7.el9.x86_64                           28/52 
  Verifying        : emacs-filesystem-1:27.2-9.el9.noarch                 29/52 
  Verifying        : automake-1.16.2-8.el9.noarch                         30/52 
  Verifying        : zlib-devel-1.2.11-40.el9.x86_64                      31/52 
  Verifying        : gcc-plugin-annobin-11.4.1-3.el9.x86_64               32/52 
  Verifying        : perl-Benchmark-1.23-481.el9.noarch                   33/52 
  Verifying        : perl-FindBin-1.51-481.el9.noarch                     34/52 
  Verifying        : systemtap-sdt-devel-5.0-4.el9.x86_64                 35/52 
  Verifying        : annobin-12.31-2.el9.x86_64                           36/52 
  Verifying        : cpp-11.4.1-3.el9.x86_64                              37/52 
  Verifying        : llvm-libs-17.0.6-5.el9.x86_64                        38/52 
  Verifying        : perl-AutoSplit-5.74-481.el9.noarch                   39/52 
  Verifying        : perl-ExtUtils-Constant-0.25-481.el9.noarch           40/52 
  Verifying        : perl-ExtUtils-Embed-1.35-481.el9.noarch              41/52 
  Verifying        : perl-File-Compare-1.100.600-481.el9.noarch           42/52 
  Verifying        : perl-File-Copy-2.34-481.el9.noarch                   43/52 
  Verifying        : perl-File-Find-1.37-481.el9.noarch                   44/52 
  Verifying        : perl-devel-4:5.32.1-481.el9.x86_64                   45/52 
  Verifying        : perl-lib-0.65-481.el9.x86_64                         46/52 
  Verifying        : perl-locale-1.09-481.el9.noarch                      47/52 
  Verifying        : gcc-11.4.1-3.el9.x86_64                              48/52 
  Verifying        : perl-DynaLoader-1.47-481.el9.x86_64                  49/52 
  Verifying        : kernel-headers-5.14.0-427.18.1.el9_4.x86_64          50/52 
  Verifying        : glibc-devel-2.34-100.el9_4.2.x86_64                  51/52 
  Verifying        : glibc-headers-2.34-100.el9_4.2.x86_64                52/52 
Installed products updated.

Installed:
  annobin-12.31-2.el9.x86_64                                                    
  autoconf-2.69-38.el9.noarch                                                   
  automake-1.16.2-8.el9.noarch                                                  
  cpp-11.4.1-3.el9.x86_64                                                       
  emacs-filesystem-1:27.2-9.el9.noarch                                          
  expat-2.5.0-2.el9_4.x86_64                                                    
  gcc-11.4.1-3.el9.x86_64                                                       
  gcc-plugin-annobin-11.4.1-3.el9.x86_64                                        
  glibc-devel-2.34-100.el9_4.2.x86_64                                           
  glibc-headers-2.34-100.el9_4.2.x86_64                                         
  gsl-2.6-7.el9.x86_64                                                          
  gsl-devel-2.6-7.el9.x86_64                                                    
  htslib-1.20-1.el9.x86_64                                                      
  htslib-devel-1.20-1.el9.x86_64                                                
  htslib-tools-1.20-1.el9.x86_64                                                
  kernel-headers-5.14.0-427.18.1.el9_4.x86_64                                   
  libedit-3.1-38.20210216cvs.el9.x86_64                                         
  libmpc-1.2.1-4.el9.x86_64                                                     
  libxcrypt-devel-4.4.18-3.el9.x86_64                                           
  llvm-libs-17.0.6-5.el9.x86_64                                                 
  m4-1.4.19-1.el9.x86_64                                                        
  make-1:4.3-8.el9.x86_64                                                       
  perl-AutoSplit-5.74-481.el9.noarch                                            
  perl-Benchmark-1.23-481.el9.noarch                                            
  perl-Devel-PPPort-3.62-4.el9.x86_64                                           
  perl-DynaLoader-1.47-481.el9.x86_64                                           
  perl-ExtUtils-Command-2:7.60-3.el9.noarch                                     
  perl-ExtUtils-Constant-0.25-481.el9.noarch                                    
  perl-ExtUtils-Embed-1.35-481.el9.noarch                                       
  perl-ExtUtils-Install-2.20-4.el9.noarch                                       
  perl-ExtUtils-MakeMaker-2:7.60-3.el9.noarch                                   
  perl-ExtUtils-Manifest-1:1.73-4.el9.noarch                                    
  perl-ExtUtils-ParseXS-1:3.40-460.el9.noarch                                   
  perl-File-Compare-1.100.600-481.el9.noarch                                    
  perl-File-Copy-2.34-481.el9.noarch                                            
  perl-File-Find-1.37-481.el9.noarch                                            
  perl-FindBin-1.51-481.el9.noarch                                              
  perl-Test-Harness-1:3.42-461.el9.noarch                                       
  perl-Thread-Queue-3.14-460.el9.noarch                                         
  perl-devel-4:5.32.1-481.el9.x86_64                                            
  perl-lib-0.65-481.el9.x86_64                                                  
  perl-locale-1.09-481.el9.noarch                                               
  perl-threads-1:2.25-460.el9.x86_64                                            
  perl-threads-shared-1.61-460.el9.x86_64                                       
  perl-version-7:0.99.28-4.el9.x86_64                                           
  python3-3.9.18-3.el9.x86_64                                                   
  python3-libs-3.9.18-3.el9.x86_64                                              
  python3-pip-wheel-21.2.3-8.el9.noarch                                         
  python3-pyparsing-2.4.7-9.el9.noarch                                          
  python3-setuptools-wheel-53.0.0-12.el9.noarch                                 
  systemtap-sdt-devel-5.0-4.el9.x86_64                                          
  zlib-devel-1.2.11-40.el9.x86_64                                               

Complete!
Finish: build setup for bcftools-1.20-1.el9.src.rpm
Start: rpmbuild bcftools-1.20-1.el9.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1717372800
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.lhgRJu
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf bcftools-1.20
+ /usr/bin/bzip2 -dc /builddir/build/SOURCES/bcftools-1.20.tar.bz2
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd bcftools-1.20
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ sed -i '1s|/usr/bin/env perl|/usr/bin/perl|' misc/color-chrs.pl misc/demo-flt.pl misc/run-roh.pl misc/vcfutils.pl misc/plot-vcfstats
+ sed -i '1s|/usr/bin/env python3\{0,1\}|/usr/bin/python3|' misc/gff2gff.py misc/guess-ploidy.py misc/plot-roh.py
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.xscch1
+ umask 022
+ cd /builddir/build/BUILD
+ cd bcftools-1.20
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']'
++ find . -type f -name configure -print
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.20/configure
+ diff -u ./htslib-1.20/configure.backup ./htslib-1.20/configure
+ mv ./htslib-1.20/configure.backup ./htslib-1.20/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.20/configure
+ diff -u ./htslib-1.20/configure.backup ./htslib-1.20/configure
+ mv ./htslib-1.20/configure.backup ./htslib-1.20/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.20/configure
+ diff -u ./htslib-1.20/configure.backup ./htslib-1.20/configure
+ mv ./htslib-1.20/configure.backup ./htslib-1.20/configure
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.20/configure
+ diff -u ./htslib-1.20/configure.backup ./htslib-1.20/configure
+ mv ./htslib-1.20/configure.backup ./htslib-1.20/configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.20/configure
+ diff -u ./htslib-1.20/configure.backup ./htslib-1.20/configure
+ mv ./htslib-1.20/configure.backup ./htslib-1.20/configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./htslib-1.20/config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./htslib-1.20/config.sub
++ basename ./htslib-1.20/config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./htslib-1.20/config.sub
'/usr/lib/rpm/redhat/config.sub' -> './htslib-1.20/config.sub'
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./htslib-1.20/config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./htslib-1.20/config.guess
++ basename ./htslib-1.20/config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./htslib-1.20/config.guess
'/usr/lib/rpm/redhat/config.guess' -> './htslib-1.20/config.guess'
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
+ ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' --prefix=/usr --with-htslib=system --enable-perl-filters --enable-libgsl '--with-bcf-plugin-path=/usr/local/libexec/bcftools:$(plugindir)'
checking for x86_64-redhat-linux-gnu-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for gcc option to enable large file support... none needed
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking shared library type... plain .so
checking for library containing dlopen... none required
checking if the compiler accepts -rdynamic... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for gsl/gsl_version.h... yes
checking for library containing cblas_dgemm... -lgslcblas
checking for gsl_multifit_gradient in -lgsl... yes
configure: removing -specs=...redhat-hardened... from Perl options
checking for library containing Perl_call_pv... -lperl
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
configure: License has been changed to GPL.

Linking against the GNU scientific library requires that the resulting
binary is licensed using the GNU General Public License.  In particular,
this means you will have to follow the terms of this license in order
to distribute binary copies.  For more information see the INSTALL file.

Text of the GNU General Public License can be found in the LICENSE file,
or at http://www.gnu.org/copyleft/gpl.html

Information on the GNU Scientific Library, including the rationale for
its choice of license can be found at https://www.gnu.org/software/gsl/

+ /usr/bin/make -O -j2 V=1 VERBOSE=1
echo '#define BCFTOOLS_VERSION "1.20"' > version.h
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o tabix.o tabix.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfindex.o vcfindex.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfisec.o vcfisec.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfstats.o vcfstats.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfquery.o vcfquery.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcffilter.o vcffilter.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfmerge.o vcfmerge.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfsom.o vcfsom.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -c -o filter.o filter.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfnorm.o vcfnorm.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfgtcheck.o vcfgtcheck.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfview.o vcfview.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfroh.o vcfroh.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfconcat.o vcfconcat.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfannotate.o vcfannotate.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfcall.o vcfcall.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcmp.o vcmp.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o gvcf.o gvcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o mcall.o mcall.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o reheader.o reheader.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfconvert.o vcfconvert.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o tsv2vcf.o tsv2vcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o convert.o convert.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfhead.o vcfhead.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfcnv.o vcfcnv.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o HMM.o HMM.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o ploidy.o ploidy.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o bin.o bin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o consensus.o consensus.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o version.o version.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o hclust.o hclust.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o smpl_ilist.o smpl_ilist.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o regidx.o regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfbuf.o vcfbuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o mpileup.o mpileup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o csq.o csq.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o bam2bcf.o bam2bcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o bam2bcf_iaux.o bam2bcf_iaux.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o read_consensus.o read_consensus.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o bam2bcf_edlib.o bam2bcf_edlib.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o vcfsort.o vcfsort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o cols.o cols.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o bam_sample.o bam_sample.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o dist.o dist.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o extsort.o extsort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o ccall.o ccall.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o em.o em.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o abuf.o abuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o kmin.o kmin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o prob1.o prob1.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o str_finder.o str_finder.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o edlib.o edlib.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o polysomy.o polysomy.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o gff.o gff.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.   -DPLUGINPATH='"/usr/local/libexec/bcftools:/usr/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o peakfit.o peakfit.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o test/test-rbuf.o test/test-rbuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -c -o test/test-regidx.o test/test-regidx.c
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/GTsubset.so version.c plugins/GTsubset.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/GTisec.so version.c plugins/GTisec.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/add-variantkey.so version.c plugins/add-variantkey.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/af-dist.so bin.c version.c plugins/af-dist.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/allele-length.so version.c plugins/allele-length.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/check-ploidy.so version.c plugins/check-ploidy.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/check-sparsity.so version.c plugins/check-sparsity.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/counts.so version.c plugins/counts.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/contrast.so version.c plugins/contrast.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/dosage.so version.c plugins/dosage.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/fill-tags.so version.c plugins/fill-tags.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/fixref.so version.c plugins/fixref.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/frameshifts.so version.c plugins/frameshifts.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/gvcfz.so version.c plugins/gvcfz.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/impute-info.so version.c plugins/impute-info.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/indel-stats.so version.c plugins/indel-stats.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/missing2ref.so version.c plugins/missing2ref.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/mendelian2.so version.c plugins/mendelian2.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/parental-origin.so version.c plugins/parental-origin.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/prune.so version.c plugins/prune.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/scatter.so version.c plugins/scatter.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/setGT.so version.c plugins/setGT.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/smpl-stats.so version.c plugins/smpl-stats.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/split.so version.c plugins/split.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/tag2tag.so version.c plugins/tag2tag.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/split-vep.so version.c plugins/split-vep.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/trio-stats.so version.c plugins/trio-stats.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/variant-distance.so version.c plugins/variant-distance.c 
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.   -DUSE_GPL -c -o main.o main.c
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c 
gcc -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o test/test-rbuf test/test-rbuf.o -lz  
gcc  -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz  
gcc -rdynamic  -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o read_consensus.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o polysomy.o peakfit.o vcfplugin.o -lhts -lm -lz   -lgsl -lgslcblas -Wl,--enable-new-dtags -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fstack-protector-strong -L/usr/local/lib -L/usr/lib64/perl5/CORE -lperl -lpthread -lresolv -ldl -lm -lcrypt -lutil -lc -lpthread
lto-wrapper: warning: using serial compilation of 19 LTRANS jobs
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.tNmgt2
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64
++ dirname /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64
+ cd bcftools-1.20
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/bin /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/share/man/man1 /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools
/usr/bin/install -p bcftools /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/bin
/usr/bin/install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/bin
/usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/share/man/man1
/usr/bin/install -p plugins/*.so /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.20-1.el9 --unique-debug-suffix -1.20-1.el9.x86_64 --unique-debug-src-base bcftools-1.20-1.el9.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/bcftools-1.20
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/bin/bcftools
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/GTisec.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/GTsubset.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/ad-bias.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/add-variantkey.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/af-dist.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/allele-length.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/check-ploidy.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/check-sparsity.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/color-chrs.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/contrast.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/counts.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/dosage.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/fill-AN-AC.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/fill-from-fasta.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/fill-tags.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/fixploidy.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/fixref.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/frameshifts.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/guess-ploidy.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/gvcfz.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/impute-info.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/indel-stats.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/mendelian2.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/isecGT.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/missing2ref.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/parental-origin.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/prune.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/remove-overlaps.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/scatter.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/setGT.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/smpl-stats.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/split-vep.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/split.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/tag2tag.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/trio-dnm2.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/trio-stats.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/trio-switch-rate.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/variant-distance.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/libexec/bcftools/variantkey-hex.so
original debug info size: 6656kB, size after compression: 5720kB
/usr/bin/sepdebugcrcfix: Updated 40 CRC32s, 0 CRC32s did match.
6174 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.H8ZsZW
+ umask 022
+ cd /builddir/build/BUILD
+ cd bcftools-1.20
+ ldd bcftools
+ grep -E '/lib(64)?/libhts\.so\.'
	libhts.so.3 => /lib64/libhts.so.3 (0x00007fc796770000)
+ make test
./test/test-rbuf
Inserted 1-9 starting at offset 5:
  5  6  7  8  9  0  1  2  3
  1  2  3  4  5  6  7  8  9
4th is 4
Deleting 1-2:
  7  8  9  0  1  2  3
  3  4  5  6  7  8  9
Prepending 0-8:
  8  9  0  1  2  3  4  5  6  7
  8  7  6  5  4  3  2  1  0  3
Expanding:
  8  9 10 11 12 13 14 15 16 17
  8  7  6  5  4  3  2  1  0  3
./test/test-regidx
REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-}
./test/test.pl: module IO::Pty not found; skipping usage tests
test_usage:
	bcftools
test_tabix:
	tabix /tmp/Uf6bgVvuEA/merge.a.vcf.gz 2:3199812-3199812
.. ok

test_tabix:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -H /tmp/Uf6bgVvuEA/merge.a.bcf 2:3199812-3199812
.. ok

test_tabix:
	tabix /tmp/Uf6bgVvuEA/merge.a.vcf.gz 1:3000151-3000151
.. ok

test_tabix:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -H /tmp/Uf6bgVvuEA/merge.a.bcf 1:3000151-3000151
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -H /tmp/Uf6bgVvuEA/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -H /tmp/Uf6bgVvuEA/large_chrom_csi_limit.bcf chr20:1-2147483647
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -H /tmp/Uf6bgVvuEA/large_chrom_csi_limit.bcf chr20:1-2147483647
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -H /tmp/Uf6bgVvuEA/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -H /tmp/Uf6bgVvuEA/large_chrom_csi_limit.bcf chr20:1-2147483647
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -H /tmp/Uf6bgVvuEA/large_chrom_csi_limit.vcf.gz chr20
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -H /tmp/Uf6bgVvuEA/large_chrom_csi_limit.bcf chr20
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -H /tmp/Uf6bgVvuEA/large_chrom_csi_limit.bcf chr20
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -H /tmp/Uf6bgVvuEA/large_chrom_csi_limit.vcf.gz chr20
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -H /tmp/Uf6bgVvuEA/large_chrom_csi_limit.bcf chr20
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -s /tmp/Uf6bgVvuEA/idx.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -s /tmp/Uf6bgVvuEA/idx.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -s /tmp/Uf6bgVvuEA/idx.bcf
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -n /tmp/Uf6bgVvuEA/idx.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -n /tmp/Uf6bgVvuEA/idx.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -n /tmp/Uf6bgVvuEA/idx.vcf.gz.csi
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -n /tmp/Uf6bgVvuEA/idx.bcf
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -n /tmp/Uf6bgVvuEA/idx.bcf.csi
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -s /tmp/Uf6bgVvuEA/empty.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -s /tmp/Uf6bgVvuEA/empty.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -s /tmp/Uf6bgVvuEA/empty.bcf
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -n /tmp/Uf6bgVvuEA/empty.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -n /tmp/Uf6bgVvuEA/empty.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -n /tmp/Uf6bgVvuEA/empty.vcf.gz.csi
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -n /tmp/Uf6bgVvuEA/empty.bcf
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.20/bcftools index -n /tmp/Uf6bgVvuEA/empty.bcf.csi
.. ok

test_vcf_check:
	/builddir/build/BUILD/bcftools-1.20/bcftools stats -s - /tmp/Uf6bgVvuEA/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
.. ok

test_vcf_check:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/check.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
.. ok

test_vcf_check_merge:
	/builddir/build/BUILD/bcftools-1.20/misc/plot-vcfstats -m /tmp/Uf6bgVvuEA/check.1.chk /tmp/Uf6bgVvuEA/check.2.chk /tmp/Uf6bgVvuEA/check.3.chk /tmp/Uf6bgVvuEA/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
.. ok

test_vcf_stats:
	/builddir/build/BUILD/bcftools-1.20/bcftools stats -s -  /tmp/Uf6bgVvuEA/stats.a.vcf.gz /tmp/Uf6bgVvuEA/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID	'
.. ok

test_vcf_stats:
	/builddir/build/BUILD/bcftools-1.20/bcftools stats -s B  /tmp/Uf6bgVvuEA/stats.a.vcf.gz /tmp/Uf6bgVvuEA/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID	'
.. ok

test_vcf_stats:
	/builddir/build/BUILD/bcftools-1.20/bcftools stats -s -  /tmp/Uf6bgVvuEA/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID	'
.. ok

test_vcf_stats:
	/builddir/build/BUILD/bcftools-1.20/bcftools stats -s - -i 'type="snp"'  /tmp/Uf6bgVvuEA/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID	'
.. ok

test_vcf_stats:
	/builddir/build/BUILD/bcftools-1.20/bcftools stats -s -  /tmp/Uf6bgVvuEA/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID	'
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -n =2 /tmp/Uf6bgVvuEA/isec.a.vcf.gz /tmp/Uf6bgVvuEA/isec.b.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -Ob -n =2 /tmp/Uf6bgVvuEA/isec.a.vcf.gz /tmp/Uf6bgVvuEA/isec.b.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/Uf6bgVvuEA/isec.a.vcf.gz /tmp/Uf6bgVvuEA/isec.b.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/Uf6bgVvuEA/isec.a.vcf.gz /tmp/Uf6bgVvuEA/isec.b.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -n =2 -c both /tmp/Uf6bgVvuEA/isec.a.vcf.gz /tmp/Uf6bgVvuEA/isec.b.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -Ob -n =2 -c both /tmp/Uf6bgVvuEA/isec.a.vcf.gz /tmp/Uf6bgVvuEA/isec.b.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -n =2 -c any /tmp/Uf6bgVvuEA/isec.a.vcf.gz /tmp/Uf6bgVvuEA/isec.b.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -Ob -n =2 -c any /tmp/Uf6bgVvuEA/isec.a.vcf.gz /tmp/Uf6bgVvuEA/isec.b.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -C -c any /tmp/Uf6bgVvuEA/isec.a.vcf.gz /tmp/Uf6bgVvuEA/isec.b.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -Ob -C -c any /tmp/Uf6bgVvuEA/isec.a.vcf.gz /tmp/Uf6bgVvuEA/isec.b.vcf.gz
.. ok

test_vcf_isec2:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec --no-version   -T /tmp/Uf6bgVvuEA/isec.tab.gz /tmp/Uf6bgVvuEA/isec.a.vcf.gz
.. ok

test_vcf_isec2:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -Ob  -T /tmp/Uf6bgVvuEA/isec.tab.gz /tmp/Uf6bgVvuEA/isec.a.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/Uf6bgVvuEA/isec-miss.1.1.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.1.2.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.1.3.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/Uf6bgVvuEA/isec-miss.1.1.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.1.2.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.1.3.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -R /builddir/build/BUILD/bcftools-1.20/test/isec-miss.1.regs.txt -n +1 /tmp/Uf6bgVvuEA/isec-miss.1.1.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.1.2.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.1.3.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.20/test/isec-miss.1.regs.txt -n +1 /tmp/Uf6bgVvuEA/isec-miss.1.1.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.1.2.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.1.3.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/Uf6bgVvuEA/isec-miss.2.1.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.2.2.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.2.3.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/Uf6bgVvuEA/isec-miss.2.1.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.2.2.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.2.3.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -R /builddir/build/BUILD/bcftools-1.20/test/isec-miss.1.regs.txt -n +1 /tmp/Uf6bgVvuEA/isec-miss.2.1.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.2.2.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.2.3.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.20/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.20/test/isec-miss.1.regs.txt -n +1 /tmp/Uf6bgVvuEA/isec-miss.2.1.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.2.2.vcf.gz /tmp/Uf6bgVvuEA/isec-miss.2.3.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -i AF:join /tmp/Uf6bgVvuEA/merge.join.a.vcf.gz /tmp/Uf6bgVvuEA/merge.join.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -i AF:join /tmp/Uf6bgVvuEA/merge.join.a.vcf.gz /tmp/Uf6bgVvuEA/merge.join.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -i AF:join /tmp/Uf6bgVvuEA/merge.join.a.bcf /tmp/Uf6bgVvuEA/merge.join.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -i AF:join /tmp/Uf6bgVvuEA/merge.join.a.bcf /tmp/Uf6bgVvuEA/merge.join.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-single /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-single /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-single /tmp/Uf6bgVvuEA/merge.LPL.a.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-single /tmp/Uf6bgVvuEA/merge.LPL.a.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.b.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.b.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples /tmp/Uf6bgVvuEA/merge.LPL.a.bcf /tmp/Uf6bgVvuEA/merge.LPL.b.bcf /tmp/Uf6bgVvuEA/merge.LPL.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/Uf6bgVvuEA/merge.LPL.a.bcf /tmp/Uf6bgVvuEA/merge.LPL.b.bcf /tmp/Uf6bgVvuEA/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -L 1 /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.b.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.b.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -L 1 /tmp/Uf6bgVvuEA/merge.LPL.a.bcf /tmp/Uf6bgVvuEA/merge.LPL.b.bcf /tmp/Uf6bgVvuEA/merge.LPL.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/Uf6bgVvuEA/merge.LPL.a.bcf /tmp/Uf6bgVvuEA/merge.LPL.b.bcf /tmp/Uf6bgVvuEA/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -L 2 /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.b.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.b.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -L 2 /tmp/Uf6bgVvuEA/merge.LPL.a.bcf /tmp/Uf6bgVvuEA/merge.LPL.b.bcf /tmp/Uf6bgVvuEA/merge.LPL.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/Uf6bgVvuEA/merge.LPL.a.bcf /tmp/Uf6bgVvuEA/merge.LPL.b.bcf /tmp/Uf6bgVvuEA/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -L 3 /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.b.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.b.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -L 3 /tmp/Uf6bgVvuEA/merge.LPL.a.bcf /tmp/Uf6bgVvuEA/merge.LPL.b.bcf /tmp/Uf6bgVvuEA/merge.LPL.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/Uf6bgVvuEA/merge.LPL.a.bcf /tmp/Uf6bgVvuEA/merge.LPL.b.bcf /tmp/Uf6bgVvuEA/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -L 4 /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.b.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.b.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -L 4 /tmp/Uf6bgVvuEA/merge.LPL.a.bcf /tmp/Uf6bgVvuEA/merge.LPL.b.bcf /tmp/Uf6bgVvuEA/merge.LPL.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/Uf6bgVvuEA/merge.LPL.a.bcf /tmp/Uf6bgVvuEA/merge.LPL.b.bcf /tmp/Uf6bgVvuEA/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -L 5 /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.b.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/Uf6bgVvuEA/merge.LPL.a.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.b.vcf.gz /tmp/Uf6bgVvuEA/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -L 5 /tmp/Uf6bgVvuEA/merge.LPL.a.bcf /tmp/Uf6bgVvuEA/merge.LPL.b.bcf /tmp/Uf6bgVvuEA/merge.LPL.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/Uf6bgVvuEA/merge.LPL.a.bcf /tmp/Uf6bgVvuEA/merge.LPL.b.bcf /tmp/Uf6bgVvuEA/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples /tmp/Uf6bgVvuEA/merge.a.vcf.gz /tmp/Uf6bgVvuEA/merge.b.vcf.gz /tmp/Uf6bgVvuEA/merge.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/Uf6bgVvuEA/merge.a.vcf.gz /tmp/Uf6bgVvuEA/merge.b.vcf.gz /tmp/Uf6bgVvuEA/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples /tmp/Uf6bgVvuEA/merge.a.bcf /tmp/Uf6bgVvuEA/merge.b.bcf /tmp/Uf6bgVvuEA/merge.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/Uf6bgVvuEA/merge.a.bcf /tmp/Uf6bgVvuEA/merge.b.bcf /tmp/Uf6bgVvuEA/merge.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -Fx /tmp/Uf6bgVvuEA/merge.a.vcf.gz /tmp/Uf6bgVvuEA/merge.b.vcf.gz /tmp/Uf6bgVvuEA/merge.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -Fx /tmp/Uf6bgVvuEA/merge.a.vcf.gz /tmp/Uf6bgVvuEA/merge.b.vcf.gz /tmp/Uf6bgVvuEA/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -Fx /tmp/Uf6bgVvuEA/merge.a.bcf /tmp/Uf6bgVvuEA/merge.b.bcf /tmp/Uf6bgVvuEA/merge.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -Fx /tmp/Uf6bgVvuEA/merge.a.bcf /tmp/Uf6bgVvuEA/merge.b.bcf /tmp/Uf6bgVvuEA/merge.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -0 /tmp/Uf6bgVvuEA/merge.a.vcf.gz /tmp/Uf6bgVvuEA/merge.b.vcf.gz /tmp/Uf6bgVvuEA/merge.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -0 /tmp/Uf6bgVvuEA/merge.a.vcf.gz /tmp/Uf6bgVvuEA/merge.b.vcf.gz /tmp/Uf6bgVvuEA/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -0 /tmp/Uf6bgVvuEA/merge.a.bcf /tmp/Uf6bgVvuEA/merge.b.bcf /tmp/Uf6bgVvuEA/merge.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -0 /tmp/Uf6bgVvuEA/merge.a.bcf /tmp/Uf6bgVvuEA/merge.b.bcf /tmp/Uf6bgVvuEA/merge.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -m none /tmp/Uf6bgVvuEA/merge.2.a.vcf.gz /tmp/Uf6bgVvuEA/merge.2.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m none /tmp/Uf6bgVvuEA/merge.2.a.vcf.gz /tmp/Uf6bgVvuEA/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -m none /tmp/Uf6bgVvuEA/merge.2.a.bcf /tmp/Uf6bgVvuEA/merge.2.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m none /tmp/Uf6bgVvuEA/merge.2.a.bcf /tmp/Uf6bgVvuEA/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -m both /tmp/Uf6bgVvuEA/merge.2.a.vcf.gz /tmp/Uf6bgVvuEA/merge.2.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m both /tmp/Uf6bgVvuEA/merge.2.a.vcf.gz /tmp/Uf6bgVvuEA/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -m both /tmp/Uf6bgVvuEA/merge.2.a.bcf /tmp/Uf6bgVvuEA/merge.2.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m both /tmp/Uf6bgVvuEA/merge.2.a.bcf /tmp/Uf6bgVvuEA/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -m all /tmp/Uf6bgVvuEA/merge.2.a.vcf.gz /tmp/Uf6bgVvuEA/merge.2.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m all /tmp/Uf6bgVvuEA/merge.2.a.vcf.gz /tmp/Uf6bgVvuEA/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -m all /tmp/Uf6bgVvuEA/merge.2.a.bcf /tmp/Uf6bgVvuEA/merge.2.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m all /tmp/Uf6bgVvuEA/merge.2.a.bcf /tmp/Uf6bgVvuEA/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/Uf6bgVvuEA/merge.3.a.vcf.gz /tmp/Uf6bgVvuEA/merge.3.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/Uf6bgVvuEA/merge.3.a.vcf.gz /tmp/Uf6bgVvuEA/merge.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/Uf6bgVvuEA/merge.3.a.bcf /tmp/Uf6bgVvuEA/merge.3.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/Uf6bgVvuEA/merge.3.a.bcf /tmp/Uf6bgVvuEA/merge.3.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -m id /tmp/Uf6bgVvuEA/merge.4.a.vcf.gz /tmp/Uf6bgVvuEA/merge.4.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m id /tmp/Uf6bgVvuEA/merge.4.a.vcf.gz /tmp/Uf6bgVvuEA/merge.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples -m id /tmp/Uf6bgVvuEA/merge.4.a.bcf /tmp/Uf6bgVvuEA/merge.4.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m id /tmp/Uf6bgVvuEA/merge.4.a.bcf /tmp/Uf6bgVvuEA/merge.4.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/gvcf.merge.1.vcf.gz /tmp/Uf6bgVvuEA/gvcf.merge.2.vcf.gz /tmp/Uf6bgVvuEA/gvcf.merge.3.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/gvcf.merge.1.vcf.gz /tmp/Uf6bgVvuEA/gvcf.merge.2.vcf.gz /tmp/Uf6bgVvuEA/gvcf.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/gvcf.merge.1.bcf /tmp/Uf6bgVvuEA/gvcf.merge.2.bcf /tmp/Uf6bgVvuEA/gvcf.merge.3.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/gvcf.merge.1.bcf /tmp/Uf6bgVvuEA/gvcf.merge.2.bcf /tmp/Uf6bgVvuEA/gvcf.merge.3.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.2.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.2.b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.2.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.2.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.2.b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - -m both,* /tmp/Uf6bgVvuEA/merge.gvcf.2.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.2.b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.2.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/Uf6bgVvuEA/merge.gvcf.2.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.2.b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - -m both,** /tmp/Uf6bgVvuEA/merge.gvcf.2.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.2.b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.2.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/Uf6bgVvuEA/merge.gvcf.2.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.2.b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - -i SRC:join /tmp/Uf6bgVvuEA/merge.gvcf.3.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.3.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/Uf6bgVvuEA/merge.gvcf.3.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.4.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.4.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.4.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.4.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.4.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.4.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.4.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version  /tmp/Uf6bgVvuEA/merge.5.a.vcf.gz /tmp/Uf6bgVvuEA/merge.5.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob  /tmp/Uf6bgVvuEA/merge.5.a.vcf.gz /tmp/Uf6bgVvuEA/merge.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version  /tmp/Uf6bgVvuEA/merge.5.a.bcf /tmp/Uf6bgVvuEA/merge.5.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob  /tmp/Uf6bgVvuEA/merge.5.a.bcf /tmp/Uf6bgVvuEA/merge.5.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version  /tmp/Uf6bgVvuEA/merge.6.a.vcf.gz /tmp/Uf6bgVvuEA/merge.6.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob  /tmp/Uf6bgVvuEA/merge.6.a.vcf.gz /tmp/Uf6bgVvuEA/merge.6.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version  /tmp/Uf6bgVvuEA/merge.6.a.bcf /tmp/Uf6bgVvuEA/merge.6.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob  /tmp/Uf6bgVvuEA/merge.6.a.bcf /tmp/Uf6bgVvuEA/merge.6.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.7.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.7.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.7.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.7.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.7.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.7.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.7.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.8.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.8.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.8.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.8.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.8.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.8.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.8.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples /tmp/Uf6bgVvuEA/merge.7.a.vcf.gz /tmp/Uf6bgVvuEA/merge.7.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/Uf6bgVvuEA/merge.7.a.vcf.gz /tmp/Uf6bgVvuEA/merge.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --force-samples /tmp/Uf6bgVvuEA/merge.7.a.bcf /tmp/Uf6bgVvuEA/merge.7.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/Uf6bgVvuEA/merge.7.a.bcf /tmp/Uf6bgVvuEA/merge.7.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa /tmp/Uf6bgVvuEA/merge.gvcf.9a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9c.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9d.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa /tmp/Uf6bgVvuEA/merge.gvcf.9a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9c.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa /tmp/Uf6bgVvuEA/merge.gvcf.9a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9b.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9c.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9d.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa /tmp/Uf6bgVvuEA/merge.gvcf.9a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9b.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9c.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/Uf6bgVvuEA/merge.gvcf.9a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9c.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9d.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/Uf6bgVvuEA/merge.gvcf.9a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9c.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/Uf6bgVvuEA/merge.gvcf.9a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9b.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9c.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9d.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/Uf6bgVvuEA/merge.gvcf.9a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9b.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9c.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa /tmp/Uf6bgVvuEA/merge.gvcf.9a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9c.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9d.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9e.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa /tmp/Uf6bgVvuEA/merge.gvcf.9a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9c.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9d.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa /tmp/Uf6bgVvuEA/merge.gvcf.9a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9b.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9c.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9d.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9e.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa /tmp/Uf6bgVvuEA/merge.gvcf.9a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9b.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9c.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9d.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/Uf6bgVvuEA/merge.gvcf.9a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9c.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9d.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9e.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/Uf6bgVvuEA/merge.gvcf.9a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9c.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9d.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/Uf6bgVvuEA/merge.gvcf.9a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9b.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9c.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9d.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9e.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/Uf6bgVvuEA/merge.gvcf.9a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9b.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9c.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9d.bcf /tmp/Uf6bgVvuEA/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version  /tmp/Uf6bgVvuEA/merge.gvcf.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob  /tmp/Uf6bgVvuEA/merge.gvcf.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version  /tmp/Uf6bgVvuEA/merge.gvcf.10.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob  /tmp/Uf6bgVvuEA/merge.gvcf.10.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -m none /tmp/Uf6bgVvuEA/merge.gvcf.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/Uf6bgVvuEA/merge.gvcf.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -m none /tmp/Uf6bgVvuEA/merge.gvcf.10.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/Uf6bgVvuEA/merge.gvcf.10.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.20/test/merge.gvcf.10.fa /tmp/Uf6bgVvuEA/merge.gvcf.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -g /builddir/build/BUILD/bcftools-1.20/test/merge.gvcf.10.fa /tmp/Uf6bgVvuEA/merge.gvcf.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.20/test/merge.gvcf.10.fa /tmp/Uf6bgVvuEA/merge.gvcf.10.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -g /builddir/build/BUILD/bcftools-1.20/test/merge.gvcf.10.fa /tmp/Uf6bgVvuEA/merge.gvcf.10.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.20/test/merge.gvcf.10.fa -m none /tmp/Uf6bgVvuEA/merge.gvcf.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -g /builddir/build/BUILD/bcftools-1.20/test/merge.gvcf.10.fa -m none /tmp/Uf6bgVvuEA/merge.gvcf.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.20/test/merge.gvcf.10.fa -m none /tmp/Uf6bgVvuEA/merge.gvcf.10.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -g /builddir/build/BUILD/bcftools-1.20/test/merge.gvcf.10.fa -m none /tmp/Uf6bgVvuEA/merge.gvcf.10.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version  /tmp/Uf6bgVvuEA/merge.noidx.a.vcf.gz /tmp/Uf6bgVvuEA/merge.noidx.b.vcf.gz /tmp/Uf6bgVvuEA/merge.noidx.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob  /tmp/Uf6bgVvuEA/merge.noidx.a.vcf.gz /tmp/Uf6bgVvuEA/merge.noidx.b.vcf.gz /tmp/Uf6bgVvuEA/merge.noidx.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version  /tmp/Uf6bgVvuEA/merge.noidx.a.bcf /tmp/Uf6bgVvuEA/merge.noidx.b.bcf /tmp/Uf6bgVvuEA/merge.noidx.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob  /tmp/Uf6bgVvuEA/merge.noidx.a.bcf /tmp/Uf6bgVvuEA/merge.noidx.b.bcf /tmp/Uf6bgVvuEA/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --no-index /builddir/build/BUILD/bcftools-1.20/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.20/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.20/test/merge.noidx.c.vcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --no-index /builddir/build/BUILD/bcftools-1.20/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.20/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.20/test/merge.noidx.c.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --no-index /tmp/Uf6bgVvuEA/merge.noidx.a.bcf /tmp/Uf6bgVvuEA/merge.noidx.b.bcf /tmp/Uf6bgVvuEA/merge.noidx.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --no-index /tmp/Uf6bgVvuEA/merge.noidx.a.bcf /tmp/Uf6bgVvuEA/merge.noidx.b.bcf /tmp/Uf6bgVvuEA/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version  /tmp/Uf6bgVvuEA/merge.8.a.vcf.gz /tmp/Uf6bgVvuEA/merge.8.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob  /tmp/Uf6bgVvuEA/merge.8.a.vcf.gz /tmp/Uf6bgVvuEA/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version  /tmp/Uf6bgVvuEA/merge.8.a.bcf /tmp/Uf6bgVvuEA/merge.8.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob  /tmp/Uf6bgVvuEA/merge.8.a.bcf /tmp/Uf6bgVvuEA/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -i AN:sum,AC:sum /tmp/Uf6bgVvuEA/merge.8.a.vcf.gz /tmp/Uf6bgVvuEA/merge.8.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/Uf6bgVvuEA/merge.8.a.vcf.gz /tmp/Uf6bgVvuEA/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -i AN:sum,AC:sum /tmp/Uf6bgVvuEA/merge.8.a.bcf /tmp/Uf6bgVvuEA/merge.8.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/Uf6bgVvuEA/merge.8.a.bcf /tmp/Uf6bgVvuEA/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version  /tmp/Uf6bgVvuEA/merge.9.a.vcf.gz /tmp/Uf6bgVvuEA/merge.9.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob  /tmp/Uf6bgVvuEA/merge.9.a.vcf.gz /tmp/Uf6bgVvuEA/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version  /tmp/Uf6bgVvuEA/merge.9.a.bcf /tmp/Uf6bgVvuEA/merge.9.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob  /tmp/Uf6bgVvuEA/merge.9.a.bcf /tmp/Uf6bgVvuEA/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -i AN:sum,AC:sum /tmp/Uf6bgVvuEA/merge.9.a.vcf.gz /tmp/Uf6bgVvuEA/merge.9.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/Uf6bgVvuEA/merge.9.a.vcf.gz /tmp/Uf6bgVvuEA/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -i AN:sum,AC:sum /tmp/Uf6bgVvuEA/merge.9.a.bcf /tmp/Uf6bgVvuEA/merge.9.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/Uf6bgVvuEA/merge.9.a.bcf /tmp/Uf6bgVvuEA/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -m none /tmp/Uf6bgVvuEA/merge.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/Uf6bgVvuEA/merge.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -m none /tmp/Uf6bgVvuEA/merge.10.a.bcf /tmp/Uf6bgVvuEA/merge.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/Uf6bgVvuEA/merge.10.a.bcf /tmp/Uf6bgVvuEA/merge.10.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -m both /tmp/Uf6bgVvuEA/merge.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -m both /tmp/Uf6bgVvuEA/merge.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -m both /tmp/Uf6bgVvuEA/merge.10.a.bcf /tmp/Uf6bgVvuEA/merge.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -m both /tmp/Uf6bgVvuEA/merge.10.a.bcf /tmp/Uf6bgVvuEA/merge.10.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -m snp-ins-del /tmp/Uf6bgVvuEA/merge.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -m snp-ins-del /tmp/Uf6bgVvuEA/merge.10.a.vcf.gz /tmp/Uf6bgVvuEA/merge.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -m snp-ins-del /tmp/Uf6bgVvuEA/merge.10.a.bcf /tmp/Uf6bgVvuEA/merge.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob -m snp-ins-del /tmp/Uf6bgVvuEA/merge.10.a.bcf /tmp/Uf6bgVvuEA/merge.10.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/merge.mrules.1.a.vcf.gz /tmp/Uf6bgVvuEA/merge.mrules.1.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/merge.mrules.1.a.vcf.gz /tmp/Uf6bgVvuEA/merge.mrules.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/merge.mrules.1.a.bcf /tmp/Uf6bgVvuEA/merge.mrules.1.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/merge.mrules.1.a.bcf /tmp/Uf6bgVvuEA/merge.mrules.1.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/Uf6bgVvuEA/merge.mrules.1.a.vcf.gz /tmp/Uf6bgVvuEA/merge.mrules.1.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/Uf6bgVvuEA/merge.mrules.1.a.vcf.gz /tmp/Uf6bgVvuEA/merge.mrules.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/Uf6bgVvuEA/merge.mrules.1.a.bcf /tmp/Uf6bgVvuEA/merge.mrules.1.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/Uf6bgVvuEA/merge.mrules.1.a.bcf /tmp/Uf6bgVvuEA/merge.mrules.1.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.5.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.5.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.5.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.5.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.5.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.5.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.5.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - --merge none /tmp/Uf6bgVvuEA/merge.gvcf.5.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.5.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/Uf6bgVvuEA/merge.gvcf.5.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - --merge none /tmp/Uf6bgVvuEA/merge.gvcf.5.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.5.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/Uf6bgVvuEA/merge.gvcf.5.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.5.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.11.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.11.b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.11.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.11.a.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.11.b.vcf.gz /tmp/Uf6bgVvuEA/merge.gvcf.11.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.11.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.11.b.bcf /tmp/Uf6bgVvuEA/merge.gvcf.11.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/Uf6bgVvuEA/merge.gvcf.11.a.bcf /tmp/Uf6bgVvuEA/merge.gvcf.11.b.bcf /tmp/Uf6bgVvuEA/merge.gvcf.11.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/Uf6bgVvuEA/query.string.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/Uf6bgVvuEA/query.string.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/Uf6bgVvuEA/query.string.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/builddir/build/BUILD/bcftools-1.20/test/query.string.2.1.txt' /tmp/Uf6bgVvuEA/query.string.2.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.string.2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/builddir/build/BUILD/bcftools-1.20/test/query.string.2.1.txt'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/builddir/build/BUILD/bcftools-1.20/test/query.string.2.2.txt' /tmp/Uf6bgVvuEA/query.string.2.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.string.2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/builddir/build/BUILD/bcftools-1.20/test/query.string.2.2.txt'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f '%RSX\t%VKX\n' /tmp/Uf6bgVvuEA/query.variantkey.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.variantkey.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%RSX\t%VKX\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XRI\n' -i'XRI[*]>1111'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XRF\n' -i'XRF[*]=2e6'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[2]~"H"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[*]~"H"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/Uf6bgVvuEA/view.vectors.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/Uf6bgVvuEA/query.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/Uf6bgVvuEA/query.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/Uf6bgVvuEA/query.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/Uf6bgVvuEA/query.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/Uf6bgVvuEA/query.2.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'IINT="."'  -f'%POS %IINT\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'IINT="."'  -f'%POS %IINT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'IINT!="."' -f'%POS %IINT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -e'IINT!="."' -f'%POS %IINT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -e'IINT="."'  -f'%POS %IINT\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -e'IINT="."'  -f'%POS %IINT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'IFLT="."'  -f'%POS %IFLT\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'IFLT="."'  -f'%POS %IFLT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -e'IFLT="."'  -f'%POS %IFLT\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -e'IFLT="."'  -f'%POS %IFLT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'ISTR="."'  -f'%POS %ISTR\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'ISTR="."'  -f'%POS %ISTR\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -e'ISTR="."'  -f'%POS %ISTR\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -e'ISTR="."'  -f'%POS %ISTR\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/Uf6bgVvuEA/filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/Uf6bgVvuEA/filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/Uf6bgVvuEA/filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/Uf6bgVvuEA/filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%LINE' /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%LINE'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/Uf6bgVvuEA/query.filter-type.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/Uf6bgVvuEA/query.filter-type.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/Uf6bgVvuEA/query.filter-type.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/Uf6bgVvuEA/query.filter-type.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/Uf6bgVvuEA/query.filter-type.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/Uf6bgVvuEA/filter-missing-floats.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/Uf6bgVvuEA/filter-missing-floats.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/Uf6bgVvuEA/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/Uf6bgVvuEA/query.filter.2.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/Uf6bgVvuEA/filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/Uf6bgVvuEA/filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 |  FMT/DP="."' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 |  FMT/DP="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 &  FMT/GQ=589' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 &  FMT/GQ=589'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/Uf6bgVvuEA/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/Uf6bgVvuEA/query.filter.3.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" &  GT~"2"' /tmp/Uf6bgVvuEA/query.filter.3.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" &  GT~"2"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/Uf6bgVvuEA/query.filter.3.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS  %SAMPLE  %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/Uf6bgVvuEA/filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS  %SAMPLE  %AD\n]\n' -i'AD[:0]+AD[:1] > 12'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/Uf6bgVvuEA/query.filter.4.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.4.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.20/test/query.56.out' /tmp/Uf6bgVvuEA/view.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/view.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.20/test/query.56.out'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/Uf6bgVvuEA/query.filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/Uf6bgVvuEA/query.filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/Uf6bgVvuEA/query.filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/Uf6bgVvuEA/query.filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/Uf6bgVvuEA/query.filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/Uf6bgVvuEA/query.filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/Uf6bgVvuEA/query.gtidx.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/Uf6bgVvuEA/query.gtidx.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/Uf6bgVvuEA/query.gtidx.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B"  && FMT/TC[:GT]=="C"' /tmp/Uf6bgVvuEA/query.gtidx.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B"  && FMT/TC[:GT]=="C"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/Uf6bgVvuEA/query.gtidx.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/Uf6bgVvuEA/query.negative.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/Uf6bgVvuEA/query.negative.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/Uf6bgVvuEA/query.negative.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/Uf6bgVvuEA/query.negative.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/Uf6bgVvuEA/query.filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/Uf6bgVvuEA/query.filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/Uf6bgVvuEA/query.filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/Uf6bgVvuEA/query.filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' /tmp/Uf6bgVvuEA/query.pbinom.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.pbinom.1.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/Uf6bgVvuEA/query.filter.6.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.6.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/Uf6bgVvuEA/query.filter.8.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/Uf6bgVvuEA/query.filter.8.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/Uf6bgVvuEA/query.filter.9.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/Uf6bgVvuEA/query.filter.9.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/Uf6bgVvuEA/query.filter.13.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.13.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS  %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/Uf6bgVvuEA/query.filter.10.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS  %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS  %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/Uf6bgVvuEA/query.filter.10.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS  %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/Uf6bgVvuEA/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/Uf6bgVvuEA/query.filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/Uf6bgVvuEA/query.filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.20/test/query.smpl.11.txt /tmp/Uf6bgVvuEA/query.smpl.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.20/test/query.smpl.11.txt
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -l -S /builddir/build/BUILD/bcftools-1.20/test/query.smpl.11.txt /tmp/Uf6bgVvuEA/query.smpl.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -l -S /builddir/build/BUILD/bcftools-1.20/test/query.smpl.11.txt
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.20/test/query.smpl.11.txt /tmp/Uf6bgVvuEA/query.smpl.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.20/test/query.smpl.11.txt
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.20/test/query.smpl.11.txt /tmp/Uf6bgVvuEA/query.smpl.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.20/test/query.smpl.11.txt
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.20/test/query.smpl.txt /tmp/Uf6bgVvuEA/query.smpl.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.20/test/query.smpl.txt
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -l -S /builddir/build/BUILD/bcftools-1.20/test/query.smpl.txt /tmp/Uf6bgVvuEA/query.smpl.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -l -S /builddir/build/BUILD/bcftools-1.20/test/query.smpl.txt
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/Uf6bgVvuEA/query.filter.id.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%ID\n' -i'ID~"s12"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/Uf6bgVvuEA/query.filter.id.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%ID\n' -i'ID="rs123"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/Uf6bgVvuEA/filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER="A"' -f'%FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/Uf6bgVvuEA/filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER~"A"' -f'%FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/Uf6bgVvuEA/filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER="A;B"' -f'%FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/Uf6bgVvuEA/filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/Uf6bgVvuEA/filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/Uf6bgVvuEA/filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/Uf6bgVvuEA/filter.10.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'DP%10==2' -f'[ %DP]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/Uf6bgVvuEA/filter.13.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/filter.13.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\n]' /tmp/Uf6bgVvuEA/query.header.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\n]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\t]\n' /tmp/Uf6bgVvuEA/query.header.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\t]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/Uf6bgVvuEA/query.header.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/Uf6bgVvuEA/query.header.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/Uf6bgVvuEA/query.header.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/Uf6bgVvuEA/query.header.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/Uf6bgVvuEA/query.filter-or.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter-or.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 |  DP=2' /tmp/Uf6bgVvuEA/query.filter-or.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/query.filter-or.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 |  DP=2'
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -cx /tmp/Uf6bgVvuEA/norm.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -cx /tmp/Uf6bgVvuEA/norm.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m- /tmp/Uf6bgVvuEA/norm.split.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m- /tmp/Uf6bgVvuEA/norm.split.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m- /tmp/Uf6bgVvuEA/norm.split.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m- /tmp/Uf6bgVvuEA/norm.split.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m- --force /tmp/Uf6bgVvuEA/norm.split.3.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m- --force /tmp/Uf6bgVvuEA/norm.split.3.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m- /tmp/Uf6bgVvuEA/norm.split.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m- /tmp/Uf6bgVvuEA/norm.split.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m- --keep-sum AD /tmp/Uf6bgVvuEA/norm.split.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m- --keep-sum AD /tmp/Uf6bgVvuEA/norm.split.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m- /tmp/Uf6bgVvuEA/norm.split.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m- /tmp/Uf6bgVvuEA/norm.split.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m+ /tmp/Uf6bgVvuEA/norm.merge.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m+ /tmp/Uf6bgVvuEA/norm.merge.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m+ /tmp/Uf6bgVvuEA/norm.merge.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m+ /tmp/Uf6bgVvuEA/norm.merge.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m+ /tmp/Uf6bgVvuEA/norm.merge.3.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m+ /tmp/Uf6bgVvuEA/norm.merge.3.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m+ -s /tmp/Uf6bgVvuEA/norm.merge.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m+ -s /tmp/Uf6bgVvuEA/norm.merge.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -Nc s /tmp/Uf6bgVvuEA/norm.setref.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -Nc s /tmp/Uf6bgVvuEA/norm.setref.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version /tmp/Uf6bgVvuEA/norm.telomere.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version /tmp/Uf6bgVvuEA/norm.telomere.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d snps /tmp/Uf6bgVvuEA/norm.rmdup.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d snps /tmp/Uf6bgVvuEA/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d indels /tmp/Uf6bgVvuEA/norm.rmdup.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d indels /tmp/Uf6bgVvuEA/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d both /tmp/Uf6bgVvuEA/norm.rmdup.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d both /tmp/Uf6bgVvuEA/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d all /tmp/Uf6bgVvuEA/norm.rmdup.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d all /tmp/Uf6bgVvuEA/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d none /tmp/Uf6bgVvuEA/norm.rmdup.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d none /tmp/Uf6bgVvuEA/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d exact /tmp/Uf6bgVvuEA/norm.rmdup.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d exact /tmp/Uf6bgVvuEA/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d none /tmp/Uf6bgVvuEA/norm.rmdup.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d none /tmp/Uf6bgVvuEA/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d exact /tmp/Uf6bgVvuEA/norm.rmdup.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d exact /tmp/Uf6bgVvuEA/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d indels /tmp/Uf6bgVvuEA/norm.rmdup.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d indels /tmp/Uf6bgVvuEA/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d any /tmp/Uf6bgVvuEA/norm.rmdup.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d any /tmp/Uf6bgVvuEA/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d both /tmp/Uf6bgVvuEA/norm.rmdup.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d both /tmp/Uf6bgVvuEA/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d snps /tmp/Uf6bgVvuEA/norm.rmdup.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -d snps /tmp/Uf6bgVvuEA/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -c s -a /tmp/Uf6bgVvuEA/norm.2.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.2.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -c s -a /tmp/Uf6bgVvuEA/norm.2.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.2.fa -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -c s /tmp/Uf6bgVvuEA/norm.iupac.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.iupac.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -c s /tmp/Uf6bgVvuEA/norm.iupac.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.iupac.fa -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -c s /tmp/Uf6bgVvuEA/norm.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.3.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -c s /tmp/Uf6bgVvuEA/norm.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.3.fa -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/Uf6bgVvuEA/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m -any --force
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/Uf6bgVvuEA/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m -any --force -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/Uf6bgVvuEA/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -a
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/Uf6bgVvuEA/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -a -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/Uf6bgVvuEA/atomize.split.1.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/Uf6bgVvuEA/atomize.split.1.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/Uf6bgVvuEA/atomize.split.1.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/Uf6bgVvuEA/atomize.split.1.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/Uf6bgVvuEA/atomize.split.1.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/Uf6bgVvuEA/atomize.split.1.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/Uf6bgVvuEA/atomize.split.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/Uf6bgVvuEA/atomize.split.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/Uf6bgVvuEA/atomize.split.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/Uf6bgVvuEA/atomize.split.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . /tmp/Uf6bgVvuEA/atomize.split.3.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . /tmp/Uf6bgVvuEA/atomize.split.3.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/Uf6bgVvuEA/atomize.split.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/Uf6bgVvuEA/atomize.split.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +both /tmp/Uf6bgVvuEA/norm.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +both /tmp/Uf6bgVvuEA/norm.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +any /tmp/Uf6bgVvuEA/norm.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +any /tmp/Uf6bgVvuEA/norm.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/Uf6bgVvuEA/norm.5.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/Uf6bgVvuEA/norm.5.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps . /tmp/Uf6bgVvuEA/norm.5.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps . /tmp/Uf6bgVvuEA/norm.5.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m -any /tmp/Uf6bgVvuEA/norm.m-any.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m -any /tmp/Uf6bgVvuEA/norm.m-any.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m -any /tmp/Uf6bgVvuEA/norm.phased-split.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m -any /tmp/Uf6bgVvuEA/norm.phased-split.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +any /tmp/Uf6bgVvuEA/norm.phased-join.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +any /tmp/Uf6bgVvuEA/norm.phased-join.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI /tmp/Uf6bgVvuEA/norm.symbolic.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.symbolic.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI /tmp/Uf6bgVvuEA/norm.symbolic.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.symbolic.fa -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI /tmp/Uf6bgVvuEA/norm.symbolic.2.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.symbolic.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI /tmp/Uf6bgVvuEA/norm.symbolic.2.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.symbolic.fa -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI /tmp/Uf6bgVvuEA/norm.right-align.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.right-align.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI /tmp/Uf6bgVvuEA/norm.right-align.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.right-align.fa -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI -g /builddir/build/BUILD/bcftools-1.20/test/norm.right-align.gff /tmp/Uf6bgVvuEA/norm.right-align.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.right-align.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI -g /builddir/build/BUILD/bcftools-1.20/test/norm.right-align.gff /tmp/Uf6bgVvuEA/norm.right-align.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.right-align.fa -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/Uf6bgVvuEA/norm.atom-split-norm.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.atom-split-norm.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/Uf6bgVvuEA/norm.atom-split-norm.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/norm.atom-split-norm.fa -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m -any /tmp/Uf6bgVvuEA/norm.string-tags.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m -any /tmp/Uf6bgVvuEA/norm.string-tags.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m - /tmp/Uf6bgVvuEA/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +both
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m - /tmp/Uf6bgVvuEA/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +both -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m - /tmp/Uf6bgVvuEA/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +indels
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m - /tmp/Uf6bgVvuEA/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +indels -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m - /tmp/Uf6bgVvuEA/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +snps
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m - /tmp/Uf6bgVvuEA/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +snps -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m - /tmp/Uf6bgVvuEA/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +any
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m - /tmp/Uf6bgVvuEA/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +any -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +any /tmp/Uf6bgVvuEA/norm.merge.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +any /tmp/Uf6bgVvuEA/norm.merge.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +both /tmp/Uf6bgVvuEA/norm.merge.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.20/bcftools norm --no-version -m +both /tmp/Uf6bgVvuEA/norm.merge.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -i 'INFO/TAG=@/builddir/build/BUILD/bcftools-1.20/test/filter.string.1.txt' /tmp/Uf6bgVvuEA/filter.string.1.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -i 'INFO/TAG=@/builddir/build/BUILD/bcftools-1.20/test/filter.string.1.txt' /tmp/Uf6bgVvuEA/filter.string.1.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -i 'FMT/TAG=@/builddir/build/BUILD/bcftools-1.20/test/filter.string.1.txt' /tmp/Uf6bgVvuEA/filter.string.1.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -i 'FMT/TAG=@/builddir/build/BUILD/bcftools-1.20/test/filter.string.1.txt' /tmp/Uf6bgVvuEA/filter.string.1.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -HA /tmp/Uf6bgVvuEA/merge.gvcf.2.a.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -HAA /tmp/Uf6bgVvuEA/merge.gvcf.2.a.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r 1
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r 1 | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r 1:1-2
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r 1:1-2 | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r 1:1,1:2
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r 1:1,1:2 | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r 1:1-1
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r 1:1-1 | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1}
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1} | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1}:1-2
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1}:1-2 | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1}:1-1
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1}:1-1 | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1-1}
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1-1} | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1-1}:1-2
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1-1}:1-1
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1-1}-2
.. ok, expected non-zero status

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/weird-chr-names.vcf.gz -r {1:1-1}-2 | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok, expected non-zero status

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/Uf6bgVvuEA/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/Uf6bgVvuEA/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -f PASS -Xks NA00003 /tmp/Uf6bgVvuEA/view.vcf.gz -r20,Y
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -f PASS -Xks NA00003 /tmp/Uf6bgVvuEA/view.vcf.gz -r20,Y | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -xs NA00003 /tmp/Uf6bgVvuEA/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -xs NA00003 /tmp/Uf6bgVvuEA/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/Uf6bgVvuEA/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/Uf6bgVvuEA/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -p /tmp/Uf6bgVvuEA/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -p /tmp/Uf6bgVvuEA/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -P /tmp/Uf6bgVvuEA/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -P /tmp/Uf6bgVvuEA/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/Uf6bgVvuEA/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/Uf6bgVvuEA/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -Hu /tmp/Uf6bgVvuEA/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -GVsnps /tmp/Uf6bgVvuEA/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -GVsnps /tmp/Uf6bgVvuEA/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/Uf6bgVvuEA/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/Uf6bgVvuEA/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -s ^NA00003 /tmp/Uf6bgVvuEA/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -s ^NA00003 /tmp/Uf6bgVvuEA/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version  /tmp/Uf6bgVvuEA/view.omitgenotypes.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob  /tmp/Uf6bgVvuEA/view.omitgenotypes.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -G /tmp/Uf6bgVvuEA/view.omitgenotypes.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -G /tmp/Uf6bgVvuEA/view.omitgenotypes.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -HG /tmp/Uf6bgVvuEA/view.omitgenotypes.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -a /tmp/Uf6bgVvuEA/many.alleles.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -a /tmp/Uf6bgVvuEA/many.alleles.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -asA /tmp/Uf6bgVvuEA/view.vectors.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -asA /tmp/Uf6bgVvuEA/view.vectors.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -asB /tmp/Uf6bgVvuEA/view.vectors.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -asB /tmp/Uf6bgVvuEA/view.vectors.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -asA /tmp/Uf6bgVvuEA/view.vectors.2.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -asA /tmp/Uf6bgVvuEA/view.vectors.2.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/Uf6bgVvuEA/view.filter.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/Uf6bgVvuEA/view.filter.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/Uf6bgVvuEA/view.filter.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/Uf6bgVvuEA/view.filter.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -i'TXT0="text"' /tmp/Uf6bgVvuEA/view.filter.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.20/test/view.chrs.tab /tmp/Uf6bgVvuEA/view.chrs.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.20/test/view.chrs.tab /tmp/Uf6bgVvuEA/view.chrs.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -i 'POS>=3062917' /tmp/Uf6bgVvuEA/filter.2.vcf.gz 1:3062917-3157410
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -i 'POS>=3062917' /tmp/Uf6bgVvuEA/filter.2.vcf.gz 1:3062917-3157410 | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/Uf6bgVvuEA/idx.1.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/Uf6bgVvuEA/idx.2.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.20/test/idx.2.bed /tmp/Uf6bgVvuEA/idx.2.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.20/test/idx.3.bed /tmp/Uf6bgVvuEA/idx.3.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.20/test/idx.4.bed /tmp/Uf6bgVvuEA/idx.4.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -Ht 2 /tmp/Uf6bgVvuEA/view-t.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -Ht 3 /tmp/Uf6bgVvuEA/view-t.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/Uf6bgVvuEA/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/Uf6bgVvuEA/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/Uf6bgVvuEA/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/Uf6bgVvuEA/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/Uf6bgVvuEA/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/Uf6bgVvuEA/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/Uf6bgVvuEA/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/Uf6bgVvuEA/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/Uf6bgVvuEA/overlap.vcf.gz 
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.1.vcf -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.1.vcf     | /builddir/build/BUILD/bcftools-1.20/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.1.vcf -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.2.vcf -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.2.vcf     | /builddir/build/BUILD/bcftools-1.20/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.2.vcf -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.3.vcf -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.3.vcf     | /builddir/build/BUILD/bcftools-1.20/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.4.vcf -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.4.vcf     | /builddir/build/BUILD/bcftools-1.20/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.4.vcf -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.5.vcf -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.5.vcf     | /builddir/build/BUILD/bcftools-1.20/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.20/bcftools view /builddir/build/BUILD/bcftools-1.20/test/view64bit.5.vcf -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view -H
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -C5:nonmajor /tmp/Uf6bgVvuEA/view.minmaxac.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -c6:nonmajor /tmp/Uf6bgVvuEA/view.minmaxac.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -q0.3:major /tmp/Uf6bgVvuEA/view.minmaxac.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/Uf6bgVvuEA/view.filter.annovar.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/Uf6bgVvuEA/view.filter.annovar.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/Uf6bgVvuEA/view.filter.annovar.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -H -a /tmp/Uf6bgVvuEA/view-a.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.20/test/view.sites.txt /tmp/Uf6bgVvuEA/view.sites.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.20/test/view.sites.txt /tmp/Uf6bgVvuEA/view.sites.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.20/test/view.sites.txt.gz /tmp/Uf6bgVvuEA/view.sites.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.20/test/view.sites.txt.gz /tmp/Uf6bgVvuEA/view.sites.vcf.gz  | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.20/bcftools head /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.20/bcftools head -h 0 /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.20/bcftools head -h 1 /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.20/bcftools head -h 5 /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.20/bcftools head -h 22 /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.20/bcftools head -h 23 /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.20/bcftools head -n 0 /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.20/bcftools head -n 1 /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.20/bcftools head -n 5 /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.20/bcftools head -h 5 -n 5 < /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.vcf
.. ok

test_vcf_head2:
	/builddir/build/BUILD/bcftools-1.20/bcftools head -s0 /tmp/Uf6bgVvuEA/mpileup.2.vcf.gz
.. ok

test_vcf_head2:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -Ob /tmp/Uf6bgVvuEA/mpileup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools head -s0
.. ok

test_vcf_head2:
	/builddir/build/BUILD/bcftools-1.20/bcftools head -s1 /tmp/Uf6bgVvuEA/mpileup.2.vcf.gz
.. ok

test_vcf_head2:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -Ob /tmp/Uf6bgVvuEA/mpileup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools head -s1
.. ok

test_vcf_head2:
	/builddir/build/BUILD/bcftools-1.20/bcftools head -s2 -h2 /tmp/Uf6bgVvuEA/mpileup.2.vcf.gz
.. ok

test_vcf_head2:
	/builddir/build/BUILD/bcftools-1.20/bcftools view --no-version -Ob /tmp/Uf6bgVvuEA/mpileup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools head -s2 -h2
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.20/test/mpileup.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.20/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mg0 /builddir/build/BUILD/bcftools-1.20/test/mpileup.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mg0 /builddir/build/BUILD/bcftools-1.20/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.20/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.X.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.20/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.20/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.ped /builddir/build/BUILD/bcftools-1.20/test/mpileup.X.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.20/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.ped /builddir/build/BUILD/bcftools-1.20/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.20/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.X.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.20/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.20/test/mpileup.NA19213.NA19129.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.20/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.20/test/mpileup.NA19213.NA19129.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.20/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.20/test/mpileup.hwe.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.20/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.20/test/mpileup.hwe.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.20/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv -G /builddir/build/BUILD/bcftools-1.20/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.20/test/mpileup.hwe.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv -G /builddir/build/BUILD/bcftools-1.20/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.20/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.tab.gz  /builddir/build/BUILD/bcftools-1.20/test/mpileup.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.tab.gz  /builddir/build/BUILD/bcftools-1.20/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.2.tab.gz  /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.2.tab.gz  /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.20/test/mpileup.3.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.20/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.20/test/mpileup.3.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.20/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.20/test/mpileup.3.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.20/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.20/test/mpileup.4.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.20/test/mpileup.4.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.20/test/mpileup.5.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.20/test/mpileup.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.cals.1.tab.gz  /builddir/build/BUILD/bcftools-1.20/test/mpileup.cals.1.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.cals.1.tab.gz  /builddir/build/BUILD/bcftools-1.20/test/mpileup.cals.1.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.cals.2.tab.gz  /builddir/build/BUILD/bcftools-1.20/test/mpileup.cals.2.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/Uf6bgVvuEA/mpileup.cals.2.tab.gz  /builddir/build/BUILD/bcftools-1.20/test/mpileup.cals.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -cv /builddir/build/BUILD/bcftools-1.20/test/mpileup.c.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -cv /builddir/build/BUILD/bcftools-1.20/test/mpileup.c.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.20/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.c.X.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.20/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.20/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.ped /builddir/build/BUILD/bcftools-1.20/test/mpileup.c.X.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.20/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.ped /builddir/build/BUILD/bcftools-1.20/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.20/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.c.X.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.20/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.20/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.20/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.20/test/call-G.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.20/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.20/test/call-G.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.20/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.20/test/call-G.2.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.20/test/call-G.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -m /builddir/build/BUILD/bcftools-1.20/test/call.af-fixation.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -m /builddir/build/BUILD/bcftools-1.20/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.20/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.20/test/call.af-fixation.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.20/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.20/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.20/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.20/test/call.af-fixation.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.20/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.20/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.20/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.2.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.20/test/view.filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.20/test/filter.1.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.20/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.20/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'ALT="."' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'ALT="."' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.20/test/filter.4.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.20/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.20/test/filter.4.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.20/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'GT="A"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'GT="A"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'GT="RR"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'GT="RR"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'GT="RA"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'GT="RA"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'GT="AR"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'GT="AR"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'GT="AA"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'GT="AA"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'GT="aA"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'GT="aA"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'GT="HET"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'GT="HET"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%FR]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%FR]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%QUAL\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.20/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\t%QUAL\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.20/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.20/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.20/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.20/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.20/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.20/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.20/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.20/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.20/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.20/test/filter.7.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.20/test/filter.7.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.20/test/filter.9.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.20/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.20/test/filter.9.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.20/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.20/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.20/test/filter.10.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.20/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.20/test/filter.10.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.20/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.20/test/filter.10.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.20/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.20/test/filter.10.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.20/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.20/test/filter.1.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.20/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.20/test/filter.1.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.20/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.20/test/filter.1.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.20/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.20/test/filter.1.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.20/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.20/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_sort:
	/builddir/build/BUILD/bcftools-1.20/bcftools sort -m 0 /builddir/build/BUILD/bcftools-1.20/test/sort.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok

test_vcf_sort:
	/builddir/build/BUILD/bcftools-1.20/bcftools sort -Ob -m 0 /builddir/build/BUILD/bcftools-1.20/test/sort.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok

test_vcf_sort:
	/builddir/build/BUILD/bcftools-1.20/bcftools sort -m 1000 /builddir/build/BUILD/bcftools-1.20/test/sort.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok

test_vcf_sort:
	/builddir/build/BUILD/bcftools-1.20/bcftools sort -Ob -m 1000 /builddir/build/BUILD/bcftools-1.20/test/sort.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | /builddir/build/BUILD/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.20/test/regions.tab /tmp/Uf6bgVvuEA/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.20/test/regions.tab
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /builddir/build/BUILD/bcftools-1.20/test/regions.tab /tmp/Uf6bgVvuEA/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Uf6bgVvuEA/regions.tab.gz /tmp/Uf6bgVvuEA/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Uf6bgVvuEA/regions.tab.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/Uf6bgVvuEA/regions.tab.gz /tmp/Uf6bgVvuEA/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Uf6bgVvuEA/regions.bed /tmp/Uf6bgVvuEA/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Uf6bgVvuEA/regions.bed
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/Uf6bgVvuEA/regions.bed /tmp/Uf6bgVvuEA/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Uf6bgVvuEA/regions.bed.gz /tmp/Uf6bgVvuEA/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Uf6bgVvuEA/regions.bed.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/Uf6bgVvuEA/regions.bed.gz /tmp/Uf6bgVvuEA/regions.vcf.gz
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.20/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.20/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.20/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.20/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.20/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.20/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots.vcf.gz  -c STR,ID,QUAL,FILTER /tmp/Uf6bgVvuEA/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots.vcf.gz  -c STR,ID,QUAL,FILTER /tmp/Uf6bgVvuEA/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c ID,QUAL,FILTER,INFO,FMT /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c ID,QUAL,FILTER,INFO,FMT /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate   -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.20/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob   -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.20/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate   -x FORMAT /builddir/build/BUILD/bcftools-1.20/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob   -x FORMAT /builddir/build/BUILD/bcftools-1.20/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots4.vcf.gz  -c +INFO /tmp/Uf6bgVvuEA/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots4.vcf.gz  -c +INFO /tmp/Uf6bgVvuEA/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.20/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.20/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.20/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.20/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots11.tab.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.20/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots11.tab.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.20/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -x INFO -c INFO/IINT /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -x INFO -c INFO/IINT /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots11.vcf.gz  -c FMT /tmp/Uf6bgVvuEA/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots11.vcf.gz  -c FMT /tmp/Uf6bgVvuEA/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c FMT/newGT:=GT /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots2.vcf.gz  -c FMT/newGT:=GT /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots12.vcf.gz  -c FMT/GT:=newGT /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots12.vcf.gz  -c FMT/GT:=newGT /tmp/Uf6bgVvuEA/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.20/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.20/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.20/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.20/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.20/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.20/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate   -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.20/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob   -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.20/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.20/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.20/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.20/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.20/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.20/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate15.tab.gz  -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=<ID=FOO,Number=1,Type=String,Description="Some description">' -H '##INFO=<ID=BAR,Number=1,Type=Integer,Description="Some description">' /builddir/build/BUILD/bcftools-1.20/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate15.tab.gz  -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=<ID=FOO,Number=1,Type=String,Description="Some description">' -H '##INFO=<ID=BAR,Number=1,Type=Integer,Description="Some description">' /builddir/build/BUILD/bcftools-1.20/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate   -x FILTER /builddir/build/BUILD/bcftools-1.20/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob   -x FILTER /builddir/build/BUILD/bcftools-1.20/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.20/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.20/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.20/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.20/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate17.3.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.20/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate17.3.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.20/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate18.1.tab.gz  -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.20/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate18.1.tab.gz  -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.20/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate18.2.tab.gz  -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.20/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate18.2.tab.gz  -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.20/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate   -c INFO/FILTER:=FILTER /builddir/build/BUILD/bcftools-1.20/test/annotate19.dst.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob   -c INFO/FILTER:=FILTER /builddir/build/BUILD/bcftools-1.20/test/annotate19.dst.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER,FILTER /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER,FILTER /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=./FILTER /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=./FILTER /tmp/Uf6bgVvuEA/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate20.src.vcf.gz  -c  FMT/GT /tmp/Uf6bgVvuEA/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate20.src.vcf.gz  -c  FMT/GT /tmp/Uf6bgVvuEA/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate20.src.vcf.gz  -c +FMT/GT /tmp/Uf6bgVvuEA/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate20.src.vcf.gz  -c +FMT/GT /tmp/Uf6bgVvuEA/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate20.src.vcf.gz  -c -FMT/GT /tmp/Uf6bgVvuEA/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate20.src.vcf.gz  -c -FMT/GT /tmp/Uf6bgVvuEA/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate.multi.tab.gz  -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.20/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate.multi.tab.gz  -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.20/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate.missing-append.tab.gz  -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /builddir/build/BUILD/bcftools-1.20/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate.missing-append.tab.gz  -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /builddir/build/BUILD/bcftools-1.20/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots9.tab.gz  -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.20/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots9.tab.gz  -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.20/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate   --rename-annots /builddir/build/BUILD/bcftools-1.20/test/annotate21.txt /builddir/build/BUILD/bcftools-1.20/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob   --rename-annots /builddir/build/BUILD/bcftools-1.20/test/annotate21.txt /builddir/build/BUILD/bcftools-1.20/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate   -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /builddir/build/BUILD/bcftools-1.20/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob   -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /builddir/build/BUILD/bcftools-1.20/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate22.vcf.gz  -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/Uf6bgVvuEA/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate22.vcf.gz  -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/Uf6bgVvuEA/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate23.tab.gz  -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.20/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate23.tab.gz  -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.20/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate24.src.vcf.gz  -c XX /tmp/Uf6bgVvuEA/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate24.src.vcf.gz  -c XX /tmp/Uf6bgVvuEA/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate25.tab.gz  -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.20/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate25.tab.gz  -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.20/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate26.tab.gz  -c CHROM,POS,~POS /builddir/build/BUILD/bcftools-1.20/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate26.tab.gz  -c CHROM,POS,~POS /builddir/build/BUILD/bcftools-1.20/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.20/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.20/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.20/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.20/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.20/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.20/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.20/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.20/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.20/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.20/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.20/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.20/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.20/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.20/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /builddir/build/BUILD/bcftools-1.20/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /builddir/build/BUILD/bcftools-1.20/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots.id.vcf.gz  -c ALT /tmp/Uf6bgVvuEA/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots.id.vcf.gz  -c ALT /tmp/Uf6bgVvuEA/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots.id.vcf.gz  -c +ALT /tmp/Uf6bgVvuEA/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots.id.vcf.gz  -c +ALT /tmp/Uf6bgVvuEA/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots.id.2.vcf.gz  --pair-logic some -c +ID /tmp/Uf6bgVvuEA/annotate.id.2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots.id.2.vcf.gz  --pair-logic some -c +ID /tmp/Uf6bgVvuEA/annotate.id.2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots.id.2.vcf.gz  --pair-logic any -c +ID /tmp/Uf6bgVvuEA/annotate.id.2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots.id.2.vcf.gz  --pair-logic any -c +ID /tmp/Uf6bgVvuEA/annotate.id.2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annotate27.tab.gz  -c CHROM,POS,REF,ALT,EVIDENCE /builddir/build/BUILD/bcftools-1.20/test/annotate27.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annotate27.tab.gz  -c CHROM,POS,REF,ALT,EVIDENCE /builddir/build/BUILD/bcftools-1.20/test/annotate27.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /builddir/build/BUILD/bcftools-1.20/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /builddir/build/BUILD/bcftools-1.20/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /builddir/build/BUILD/bcftools-1.20/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /builddir/build/BUILD/bcftools-1.20/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /builddir/build/BUILD/bcftools-1.20/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /builddir/build/BUILD/bcftools-1.20/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /builddir/build/BUILD/bcftools-1.20/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /builddir/build/BUILD/bcftools-1.20/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate   -m XXX /builddir/build/BUILD/bcftools-1.20/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob   -m XXX /builddir/build/BUILD/bcftools-1.20/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots34.tab.gz  -c CHROM,FROM,TO,INFO/END -H '##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate in reference for SV">' /builddir/build/BUILD/bcftools-1.20/test/annotate34.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots34.tab.gz  -c CHROM,FROM,TO,INFO/END -H '##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate in reference for SV">' /builddir/build/BUILD/bcftools-1.20/test/annotate34.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -a /tmp/Uf6bgVvuEA/annots-mark.bed.gz  -c CHROM,FROM,TO -m TAG /builddir/build/BUILD/bcftools-1.20/test/annots-mark.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate -Ob -a /tmp/Uf6bgVvuEA/annots-mark.bed.gz  -c CHROM,FROM,TO -m TAG /builddir/build/BUILD/bcftools-1.20/test/annots-mark.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +check-ploidy --no-version /tmp/Uf6bgVvuEA/checkploidy.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +check-ploidy --no-version /tmp/Uf6bgVvuEA/checkploidy.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +check-ploidy --no-version /tmp/Uf6bgVvuEA/checkploidy.2.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +check-ploidy --no-version /tmp/Uf6bgVvuEA/checkploidy.2.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +check-ploidy --no-version /tmp/Uf6bgVvuEA/checkploidy.2.vcf.gz -- -m | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +check-ploidy --no-version /tmp/Uf6bgVvuEA/checkploidy.2.bcf -- -m | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +missing2ref --no-version /tmp/Uf6bgVvuEA/plugin1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +missing2ref --no-version /tmp/Uf6bgVvuEA/plugin1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/plugin1.vcf.gz -- -t . -n 0 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/plugin1.bcf -- -t . -n 0 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.20/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.20/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.20/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.20/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.20/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.20/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.3.vcf.gz -- -t a -n pM | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.3.bcf -- -t a -n pM | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.3.vcf.gz -- -t a -n pm | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.3.bcf -- -t a -n pm | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.3.vcf.gz -- -t a -n c:1 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.3.bcf -- -t a -n c:1 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.3.vcf.gz -- -t a -n c:"1|1" | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.3.bcf -- -t a -n c:"1|1" | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.3.vcf.gz -- -t a -n c:"m|M" | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.3.bcf -- -t a -n c:"m|M" | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.3.vcf.gz -- -t a -n c:0/1/1 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.3.bcf -- -t a -n c:0/1/1 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.4.bcf -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.4.bcf -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.5.vcf.gz -- -t a -n X | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.5.bcf -- -t a -n X | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.5.vcf.gz -- -t a -n c:0/X/X | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.5.bcf -- -t a -n c:0/X/X | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.6.vcf.gz -- -t ./x -n . | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.6.bcf -- -t ./x -n . | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.6.vcf.gz -- -t . -n . | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.6.bcf -- -t . -n . | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.6.vcf.gz -- -t r:0.5 -n . | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +setGT --no-version /tmp/Uf6bgVvuEA/setGT.6.bcf -- -t r:0.5 -n . | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-AN-AC --no-version /tmp/Uf6bgVvuEA/plugin1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-AN-AC --no-version /tmp/Uf6bgVvuEA/plugin1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +dosage /tmp/Uf6bgVvuEA/dosage.vcf.gz -- -t PL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +dosage /tmp/Uf6bgVvuEA/dosage.bcf -- -t PL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +dosage /tmp/Uf6bgVvuEA/dosage.vcf.gz -- -t GL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +dosage /tmp/Uf6bgVvuEA/dosage.bcf -- -t GL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +dosage /tmp/Uf6bgVvuEA/dosage.vcf.gz -- -t GT | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +dosage /tmp/Uf6bgVvuEA/dosage.bcf -- -t GT | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixploidy --no-version /tmp/Uf6bgVvuEA/fixploidy.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.20/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.20/test/fixploidy.ploidy | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixploidy --no-version /tmp/Uf6bgVvuEA/fixploidy.bcf -- -s /builddir/build/BUILD/bcftools-1.20/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.20/test/fixploidy.ploidy | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +guess-ploidy /tmp/Uf6bgVvuEA/view.PL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +guess-ploidy /tmp/Uf6bgVvuEA/view.PL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +guess-ploidy /tmp/Uf6bgVvuEA/view.GL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +guess-ploidy /tmp/Uf6bgVvuEA/view.GL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +tag2tag --no-version /tmp/Uf6bgVvuEA/view.GL.vcf.gz -- -r --gl-to-pl | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +tag2tag --no-version /tmp/Uf6bgVvuEA/view.GL.bcf -- -r --gl-to-pl | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +tag2tag --no-version /tmp/Uf6bgVvuEA/view.GL.vcf.gz -- --gl-to-gp | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +tag2tag --no-version /tmp/Uf6bgVvuEA/view.GL.bcf -- --gl-to-gp | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +tag2tag --no-version /tmp/Uf6bgVvuEA/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +tag2tag --no-version /tmp/Uf6bgVvuEA/view.GP.bcf -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +tag2tag --no-version /tmp/Uf6bgVvuEA/tag2tag.LPL.1.vcf.gz -- --LXX-to-XX | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +tag2tag --no-version /tmp/Uf6bgVvuEA/tag2tag.LPL.1.bcf -- --LXX-to-XX | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +tag2tag --no-version /tmp/Uf6bgVvuEA/tag2tag.LPL.1.vcf.gz -- --LXX-to-XX -r | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +tag2tag --no-version /tmp/Uf6bgVvuEA/tag2tag.LPL.1.bcf -- --LXX-to-XX -r | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +tag2tag --no-version /tmp/Uf6bgVvuEA/tag2tag.LPL.1.vcf.gz -- --LXX-to-XX -r -d AD:0,PL:255 -s 3 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +tag2tag --no-version /tmp/Uf6bgVvuEA/tag2tag.LPL.1.bcf -- --LXX-to-XX -r -d AD:0,PL:255 -s 3 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +add-variantkey /tmp/Uf6bgVvuEA/query.variantkey.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +add-variantkey /tmp/Uf6bgVvuEA/query.variantkey.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +variantkey-hex /tmp/Uf6bgVvuEA/query.variantkey.vcf.gz test/ | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +variantkey-hex /tmp/Uf6bgVvuEA/query.variantkey.bcf test/ | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +allele-length /tmp/Uf6bgVvuEA/query.nucleotide.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +allele-length /tmp/Uf6bgVvuEA/query.nucleotide.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/view.vcf.gz -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/view.bcf -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/view.vcf.gz -- -t AC -S /builddir/build/BUILD/bcftools-1.20/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/view.bcf -- -t AC -S /builddir/build/BUILD/bcftools-1.20/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/view.vcf.gz -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.20/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/view.bcf -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.20/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/many-alts.vcf.gz -- -t AN,AC | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/many-alts.bcf -- -t AN,AC | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-hemi.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-hemi.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-hemi.vcf.gz -- -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-hemi.bcf -- -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-hwe.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-hwe.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-hwe.vcf.gz -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-hwe.bcf -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-AN0.vcf.gz -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-AN0.bcf -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-VAF.vcf.gz -- -t VAF,VAF1 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-VAF.bcf -- -t VAF,VAF1 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-AD.vcf.gz -- -t 'FORMAT/DP:1=int(smpl_sum(FMT/AD))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-AD.bcf -- -t 'FORMAT/DP:1=int(smpl_sum(FMT/AD))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-AD.vcf.gz -- -t 'XX=N_PASS(FMT/AD[:0]<=10)','YY=N_PASS(FMT/AD[:0]>10)' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-tags --no-version /tmp/Uf6bgVvuEA/fill-tags-AD.bcf -- -t 'XX=N_PASS(FMT/AD[:0]<=10)','YY=N_PASS(FMT/AD[:0]>10)' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.vcf.gz  | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.bcf  | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.vcf.gz -- -H | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.bcf -- -H | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.vcf.gz -- -Hm | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.bcf -- -Hm | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.vcf.gz -- -Hmv | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.bcf -- -Hmv | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.vcf.gz -- -Hv | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.bcf -- -Hv | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.vcf.gz -- -m | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.bcf -- -m | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.vcf.gz -- -mv | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.bcf -- -mv | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.vcf.gz -- -v | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTisec /tmp/Uf6bgVvuEA/view.bcf -- -v | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-switch-rate /tmp/Uf6bgVvuEA/trio.vcf.gz -- -p /builddir/build/BUILD/bcftools-1.20/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-switch-rate /tmp/Uf6bgVvuEA/trio.bcf -- -p /builddir/build/BUILD/bcftools-1.20/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-stats /tmp/Uf6bgVvuEA/trio-stats.vcf.gz -a 1 -p /builddir/build/BUILD/bcftools-1.20/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-stats /tmp/Uf6bgVvuEA/trio-stats.bcf -a 1 -p /builddir/build/BUILD/bcftools-1.20/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-stats /tmp/Uf6bgVvuEA/trio-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.20/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-stats /tmp/Uf6bgVvuEA/trio-stats.bcf -p /builddir/build/BUILD/bcftools-1.20/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +smpl-stats /tmp/Uf6bgVvuEA/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +smpl-stats /tmp/Uf6bgVvuEA/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +indel-stats /tmp/Uf6bgVvuEA/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +indel-stats /tmp/Uf6bgVvuEA/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +indel-stats /tmp/Uf6bgVvuEA/indel-stats.vcf.gz  -p /builddir/build/BUILD/bcftools-1.20/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +indel-stats /tmp/Uf6bgVvuEA/indel-stats.bcf  -p /builddir/build/BUILD/bcftools-1.20/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +indel-stats /tmp/Uf6bgVvuEA/indel-stats.vcf.gz  -p /builddir/build/BUILD/bcftools-1.20/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +indel-stats /tmp/Uf6bgVvuEA/indel-stats.bcf  -p /builddir/build/BUILD/bcftools-1.20/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +ad-bias /tmp/Uf6bgVvuEA/ad-bias.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.20/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +ad-bias /tmp/Uf6bgVvuEA/ad-bias.bcf -- -s /builddir/build/BUILD/bcftools-1.20/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +ad-bias /tmp/Uf6bgVvuEA/ad-bias.2.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.20/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +ad-bias /tmp/Uf6bgVvuEA/ad-bias.2.bcf -- -s /builddir/build/BUILD/bcftools-1.20/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +ad-bias /tmp/Uf6bgVvuEA/ad-bias.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.20/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +ad-bias /tmp/Uf6bgVvuEA/ad-bias.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.20/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +ad-bias /tmp/Uf6bgVvuEA/ad-bias.2.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.20/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +ad-bias /tmp/Uf6bgVvuEA/ad-bias.2.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.20/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +af-dist /tmp/Uf6bgVvuEA/af-dist.vcf.gz  | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +af-dist /tmp/Uf6bgVvuEA/af-dist.bcf  | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixref /tmp/Uf6bgVvuEA/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -i /tmp/Uf6bgVvuEA/fixref.2b.vcf.gz | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixref /tmp/Uf6bgVvuEA/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -i /tmp/Uf6bgVvuEA/fixref.2b.vcf.gz | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixref /tmp/Uf6bgVvuEA/fixref.3.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.20/test/fixref.3.fa -m top | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixref /tmp/Uf6bgVvuEA/fixref.3.bcf -- -f /builddir/build/BUILD/bcftools-1.20/test/fixref.3.fa -m top | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixref /tmp/Uf6bgVvuEA/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -m ref-alt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixref /tmp/Uf6bgVvuEA/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -m ref-alt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixref /tmp/Uf6bgVvuEA/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -m flip | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixref /tmp/Uf6bgVvuEA/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -m flip | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixref /tmp/Uf6bgVvuEA/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -m flip-all | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixref /tmp/Uf6bgVvuEA/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -m flip-all | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixref /tmp/Uf6bgVvuEA/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -m swap | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fixref /tmp/Uf6bgVvuEA/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -m swap | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-from-fasta /tmp/Uf6bgVvuEA/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.20/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.20/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-from-fasta /tmp/Uf6bgVvuEA/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.20/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.20/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-from-fasta /tmp/Uf6bgVvuEA/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.20/test/aa.fa -c REF -N | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-from-fasta /tmp/Uf6bgVvuEA/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.20/test/aa.fa -c REF -N | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-from-fasta /tmp/Uf6bgVvuEA/ref.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -c REF | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +fill-from-fasta /tmp/Uf6bgVvuEA/ref.bcf -- -f /builddir/build/BUILD/bcftools-1.20/test/norm.fa -c REF | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTsubset --no-version /tmp/Uf6bgVvuEA/view.vcf.gz -- -s NA00001 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTsubset --no-version /tmp/Uf6bgVvuEA/view.bcf -- -s NA00001 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTsubset --no-version /tmp/Uf6bgVvuEA/view.vcf.gz -- -s NA00001,NA00002 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTsubset --no-version /tmp/Uf6bgVvuEA/view.bcf -- -s NA00001,NA00002 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTsubset --no-version /tmp/Uf6bgVvuEA/view.vcf.gz -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +GTsubset --no-version /tmp/Uf6bgVvuEA/view.bcf -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +mendelian2 /tmp/Uf6bgVvuEA/mendelian.vcf.gz -p child1,dad1,mom1 -md | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +mendelian2 /tmp/Uf6bgVvuEA/mendelian.bcf -p child1,dad1,mom1 -md | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +mendelian2 /tmp/Uf6bgVvuEA/mendelian.vcf.gz -p child1,dad1,mom1 -mg | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +mendelian2 /tmp/Uf6bgVvuEA/mendelian.bcf -p child1,dad1,mom1 -mg | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +mendelian2 /tmp/Uf6bgVvuEA/mendelian.vcf.gz -p child1,dad1,mom1 -me | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +mendelian2 /tmp/Uf6bgVvuEA/mendelian.bcf -p child1,dad1,mom1 -me | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +mendelian2 /tmp/Uf6bgVvuEA/mendelian.vcf.gz -p child1,dad1,mom1 -ma | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +mendelian2 /tmp/Uf6bgVvuEA/mendelian.bcf -p child1,dad1,mom1 -ma | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +mendelian2 /tmp/Uf6bgVvuEA/mendelian.vcf.gz -p child1,dad1,mom1 -mm | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +mendelian2 /tmp/Uf6bgVvuEA/mendelian.bcf -p child1,dad1,mom1 -mm | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +mendelian2 /tmp/Uf6bgVvuEA/mendelian.vcf.gz -p child1,dad1,mom1 | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +mendelian2 /tmp/Uf6bgVvuEA/mendelian.bcf -p child1,dad1,mom1 | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +contrast /tmp/Uf6bgVvuEA/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +contrast /tmp/Uf6bgVvuEA/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +contrast /tmp/Uf6bgVvuEA/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.20/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.20/test/contrast1.txt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +contrast /tmp/Uf6bgVvuEA/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.20/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.20/test/contrast1.txt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +contrast /tmp/Uf6bgVvuEA/contrast.vcf.gz -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +contrast /tmp/Uf6bgVvuEA/contrast.bcf -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +contrast /tmp/Uf6bgVvuEA/contrast.1.vcf.gz -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +contrast /tmp/Uf6bgVvuEA/contrast.1.bcf -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +contrast /tmp/Uf6bgVvuEA/contrast.1.vcf.gz -a NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +contrast /tmp/Uf6bgVvuEA/contrast.1.bcf -a NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.1.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.1.bcf -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.2.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.2.bcf -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother           | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.4.bcf -p proband,father,mother           | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.4.bcf -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.5.bcf -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.6.bcf -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother        --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.7.bcf -p proband,father,mother        --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.8.vcf.gz -p proband,father,mother  | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.8.bcf -p proband,father,mother  | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.9.vcf.gz -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.9.bcf -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.9.vcf.gz -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.9.bcf -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.10.vcf.gz -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.10.bcf -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.11.vcf.gz -p proband,father,mother | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.11.bcf -p proband,father,mother | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.11.vcf.gz -p 1X:proband,father,mother --strictly-novel | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +trio-dnm2 /tmp/Uf6bgVvuEA/trio-dnm/trio-dnm.11.bcf -p 1X:proband,father,mother --strictly-novel | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +gvcfz /tmp/Uf6bgVvuEA/gvcfz.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +gvcfz /tmp/Uf6bgVvuEA/gvcfz.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +gvcfz /tmp/Uf6bgVvuEA/gvcfz.vcf.gz -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +gvcfz /tmp/Uf6bgVvuEA/gvcfz.bcf -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +gvcfz /tmp/Uf6bgVvuEA/gvcfz.2.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +gvcfz /tmp/Uf6bgVvuEA/gvcfz.2.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +remove-overlaps /tmp/Uf6bgVvuEA/remove-overlaps.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +remove-overlaps /tmp/Uf6bgVvuEA/remove-overlaps.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +remove-overlaps /tmp/Uf6bgVvuEA/remove-overlaps.vcf.gz -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +remove-overlaps /tmp/Uf6bgVvuEA/remove-overlaps.bcf -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -s CANONICAL=YES:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -s CANONICAL=YES:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -s CANONICAL=YES:missense+ -f'%POS\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -s CANONICAL=YES:missense+ -f'%POS\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.2.vcf.gz -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.2.bcf -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.2.vcf.gz -s worst -f'%POS\t%AF\n' -a BCSQ | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.2.bcf -s worst -f'%POS\t%AF\n' -a BCSQ | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.2.vcf.gz -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.2.bcf -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.2.vcf.gz -s worst -f'%POS\t%INFO/AF\n' -a BCSQ | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.2.bcf -s worst -f'%POS\t%INFO/AF\n' -a BCSQ | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.3.vcf.gz -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.3.bcf -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.3.vcf.gz -s worst -f'[%POS\t%SAMPLE\t%GT\t%Consequence\n]' -i'GT="alt"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.3.bcf -s worst -f'[%POS\t%SAMPLE\t%GT\t%Consequence\n]' -i'GT="alt"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d -H | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d -H | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.4.bcf -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n'         -A tab -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.4.bcf -f '%POS\t%BCSQ\n'         -A tab -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -c gnomAD_NFE_AF,ALLELE_NUM          | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -c gnomAD_NFE_AF,ALLELE_NUM          | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.5.vcf.gz -s :synonymous    -c Consequence | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.5.bcf -s :synonymous    -c Consequence | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.5.vcf.gz -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.5.bcf -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.6.vcf.gz -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.6.bcf -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.6.vcf.gz -c - | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.6.bcf -c - | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.6.vcf.gz -c - -s worst | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.6.bcf -c - -s worst | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.7.vcf.gz --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.7.bcf --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.8.vcf.gz -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.8.bcf -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.8.vcf.gz         -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.8.bcf         -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.8.vcf.gz -a BCSQ -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.8.bcf -a BCSQ -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.8.vcf.gz         -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.8.bcf         -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.9.vcf.gz -a BCSQ -f '%CHROM\t%POS\t%REF\t%ALT\t%BCSQ\n' -d -A tab | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.9.bcf -a BCSQ -f '%CHROM\t%POS\t%REF\t%ALT\t%BCSQ\n' -d -A tab | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.9.vcf.gz -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.9.bcf -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.10.vcf.gz -a CSQ -f '%M_CAP_pred %M_CAP_score\n' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.10.bcf -a CSQ -f '%M_CAP_pred %M_CAP_score\n' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.10.vcf.gz -a CSQ -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.10.bcf -a CSQ -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.10.vcf.gz        -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.10.bcf        -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' -g /builddir/build/BUILD/bcftools-1.20/test/split-vep.gene-list.txt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' -g /builddir/build/BUILD/bcftools-1.20/test/split-vep.gene-list.txt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' -g /builddir/build/BUILD/bcftools-1.20/test/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' -g /builddir/build/BUILD/bcftools-1.20/test/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' -g +/builddir/build/BUILD/bcftools-1.20/test/split-vep.gene-list.txt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' -g +/builddir/build/BUILD/bcftools-1.20/test/split-vep.gene-list.txt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' -g +/builddir/build/BUILD/bcftools-1.20/test/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' -g +/builddir/build/BUILD/bcftools-1.20/test/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.broken-LoF.vcf.gz -d -f '%CHROM:%POS %Consequence %LoF_info\n' -a vep | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.broken-LoF.bcf -d -f '%CHROM:%POS %Consequence %LoF_info\n' -a vep | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.broken-LoF.vcf.gz -d -f '%CHROM:%POS %LoF_info\n' -a vep -i 'Consequence=="frameshift_variant"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.broken-LoF.bcf -d -f '%CHROM:%POS %LoF_info\n' -a vep -i 'Consequence=="frameshift_variant"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -f'%POS\n' -i'SYMBOL~"SAMD11"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -f'%POS\n' -i'SYMBOL~"SAMD11"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.vcf.gz -f'%POS\t%MAX_AF\n' -i'MAX_AF>0.999' -c MAX_AF,MAX_AF:float,MAX_AF | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.bcf -f'%POS\t%MAX_AF\n' -i'MAX_AF>0.999' -c MAX_AF,MAX_AF:float,MAX_AF | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.filter.vcf.gz -s worst -i'CSQ~"nonsense"' -f '%POS %Consequence %Feature %BIOTYPE' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.filter.bcf -s worst -i'CSQ~"nonsense"' -f '%POS %Consequence %Feature %BIOTYPE' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.filter.vcf.gz -s worst -i'CSQ~"nonsense"' -f '%POS %Consequence %Feature %BIOTYPE %CSQ' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.filter.bcf -s worst -i'CSQ~"nonsense"' -f '%POS %Consequence %Feature %BIOTYPE %CSQ' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s primary | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s primary | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL=YES | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL=YES | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL!=YES | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL!=YES | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL= | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL= | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s mane | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s mane | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s MANE_SELECT!='' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s MANE_SELECT!='' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.vcf.gz -s mane | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.bcf -s mane | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.vcf.gz -s primary | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.bcf -s primary | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.vcf.gz -s PolyPhen~damaging | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.select-tr-expr.bcf -s PolyPhen~damaging | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.types.vcf.gz -f'%cDNA_position %CDS_position %Protein_position' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.types.bcf -f'%cDNA_position %CDS_position %Protein_position' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.types.vcf.gz -f'%cDNA_position %CDS_position %Protein_position' -c cDNA_position:int,CDS_position:int,Protein_position:int | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.types.bcf -f'%cDNA_position %CDS_position %Protein_position' -c cDNA_position:int,CDS_position:int,Protein_position:int | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.filter-missing-bt2098.vcf.gz -e 'gnomad_genomes_AF >= 0.02' | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS 	 %gnomad_genomes_AF
' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.filter-missing-bt2098.bcf -e 'gnomad_genomes_AF >= 0.02' | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS 	 %gnomad_genomes_AF
' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.filter-missing-bt2098.vcf.gz -i 'gnomad_genomes_AF < 0.02 || gnomad_genomes_AF=="."' | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS 	 %gnomad_genomes_AF
' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split-vep /tmp/Uf6bgVvuEA/split-vep.filter-missing-bt2098.bcf -i 'gnomad_genomes_AF < 0.02 || gnomad_genomes_AF=="."' | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM %POS 	 %gnomad_genomes_AF
' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +parental-origin /tmp/Uf6bgVvuEA/parental-origin.vcf.gz -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +parental-origin /tmp/Uf6bgVvuEA/parental-origin.bcf -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +parental-origin /tmp/Uf6bgVvuEA/parental-origin.vcf.gz -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +parental-origin /tmp/Uf6bgVvuEA/parental-origin.bcf -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +parental-origin /tmp/Uf6bgVvuEA/parental-origin.vcf.gz -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +parental-origin /tmp/Uf6bgVvuEA/parental-origin.bcf -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +parental-origin /tmp/Uf6bgVvuEA/parental-origin.vcf.gz -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +parental-origin /tmp/Uf6bgVvuEA/parental-origin.bcf -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +parental-origin /tmp/Uf6bgVvuEA/parental-origin.vcf.gz -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +parental-origin /tmp/Uf6bgVvuEA/parental-origin.bcf -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 1 -a r2,LD,HD /tmp/Uf6bgVvuEA/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 1 -a r2,LD,HD /tmp/Uf6bgVvuEA/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 1 -a r2,LD,HD /tmp/Uf6bgVvuEA/prune.2.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 1 -a r2,LD,HD /tmp/Uf6bgVvuEA/prune.2.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/Uf6bgVvuEA/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/Uf6bgVvuEA/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 2 -a r2 -m 0.5  /tmp/Uf6bgVvuEA/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 2 -a r2 -m 0.5  /tmp/Uf6bgVvuEA/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/Uf6bgVvuEA/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/Uf6bgVvuEA/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/Uf6bgVvuEA/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/Uf6bgVvuEA/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 2bp -n 1 -N 1st /tmp/Uf6bgVvuEA/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 2bp -n 1 -N 1st /tmp/Uf6bgVvuEA/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/Uf6bgVvuEA/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/Uf6bgVvuEA/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +variant-distance /tmp/Uf6bgVvuEA/variant-distance.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +variant-distance /tmp/Uf6bgVvuEA/variant-distance.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +variant-distance -d nearest /tmp/Uf6bgVvuEA/variant-distance.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +variant-distance -d nearest /tmp/Uf6bgVvuEA/variant-distance.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +variant-distance -d fwd /tmp/Uf6bgVvuEA/variant-distance.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +variant-distance -d fwd /tmp/Uf6bgVvuEA/variant-distance.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +variant-distance -d rev /tmp/Uf6bgVvuEA/variant-distance.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +variant-distance -d rev /tmp/Uf6bgVvuEA/variant-distance.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +variant-distance -d both /tmp/Uf6bgVvuEA/variant-distance.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.20/bcftools +variant-distance -d both /tmp/Uf6bgVvuEA/variant-distance.bcf  | grep -v ^##bcftools_
.. ok

test_plugin_split:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split /builddir/build/BUILD/bcftools-1.20/test/split.1.vcf -o /tmp/Uf6bgVvuEA/split.1.1   && cd /tmp/Uf6bgVvuEA/split.1.1  && for f in A1.vcf A2.vcf A3.vcf B1.vcf B2.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.20/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.20/bcftools view -H $f; done
.. ok

test_plugin_split:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split /builddir/build/BUILD/bcftools-1.20/test/split.1.vcf -o /tmp/Uf6bgVvuEA/split.1.2 -S /builddir/build/BUILD/bcftools-1.20/test/split.smpl.1.2.txt  && cd /tmp/Uf6bgVvuEA/split.1.2  && for f in A.vcf B.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.20/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.20/bcftools view -H $f; done
.. ok

test_plugin_split:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split /builddir/build/BUILD/bcftools-1.20/test/split.1.vcf -o /tmp/Uf6bgVvuEA/split.1.3 -S /builddir/build/BUILD/bcftools-1.20/test/split.smpl.1.3.txt  && cd /tmp/Uf6bgVvuEA/split.1.3  && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.20/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.20/bcftools view -H $f; done
.. ok

test_plugin_split:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split /builddir/build/BUILD/bcftools-1.20/test/split.1.vcf -o /tmp/Uf6bgVvuEA/split.1.4 -S /builddir/build/BUILD/bcftools-1.20/test/split.smpl.1.3.txt -i 'GT[0]="alt"'  && cd /tmp/Uf6bgVvuEA/split.1.4  && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.20/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.20/bcftools view -H $f; done
.. ok

test_plugin_split:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split /builddir/build/BUILD/bcftools-1.20/test/split.1.vcf -o /tmp/Uf6bgVvuEA/split.1.5 -S /builddir/build/BUILD/bcftools-1.20/test/split.smpl.1.3.txt -i 'GT="alt"'  && cd /tmp/Uf6bgVvuEA/split.1.5  && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.20/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.20/bcftools view -H $f; done
.. ok

test_plugin_split:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split /builddir/build/BUILD/bcftools-1.20/test/split.1.vcf -o /tmp/Uf6bgVvuEA/split.1.6 -S /builddir/build/BUILD/bcftools-1.20/test/split.smpl.1.4.txt -i 'GT="alt"'  && cd /tmp/Uf6bgVvuEA/split.1.6  && for f in file1.vcf file2.vcf file3.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.20/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.20/bcftools view -H $f; done
.. ok

test_plugin_split:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split /builddir/build/BUILD/bcftools-1.20/test/split.1.vcf -o /tmp/Uf6bgVvuEA/split.1.7 -G /builddir/build/BUILD/bcftools-1.20/test/split.grp.1.1.txt  && cd /tmp/Uf6bgVvuEA/split.1.7  && for f in A.vcf A1.vcf A2.vcf B.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.20/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.20/bcftools view -H $f; done
.. ok

test_plugin_split:
	/builddir/build/BUILD/bcftools-1.20/bcftools +split /builddir/build/BUILD/bcftools-1.20/test/split.2.vcf -o /tmp/Uf6bgVvuEA/split.2.1   && cd /tmp/Uf6bgVvuEA/split.2.1  && for f in A1_A1-1.vcf A1_A1-2.vcf A1_A1.vcf B1.vcf B2.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.20/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.20/bcftools view -H $f; done
.. ok

test_plugin_scatter:
	/builddir/build/BUILD/bcftools-1.20/bcftools +scatter /builddir/build/BUILD/bcftools-1.20/test/scatter.1.vcf -o /tmp/Uf6bgVvuEA/scatter.1.1 -n 3 && cd /tmp/Uf6bgVvuEA/scatter.1.1 && cat 0.vcf 1.vcf 2.vcf | grep -v ^##
.. ok

test_plugin_scatter:
	/builddir/build/BUILD/bcftools-1.20/bcftools +scatter /builddir/build/BUILD/bcftools-1.20/test/scatter.1.vcf -o /tmp/Uf6bgVvuEA/scatter.1.2 -s 21,22 && cd /tmp/Uf6bgVvuEA/scatter.1.2 && cat 21.vcf 22.vcf | grep -v ^##
.. ok

test_plugin_scatter:
	/builddir/build/BUILD/bcftools-1.20/bcftools +scatter /builddir/build/BUILD/bcftools-1.20/test/scatter.1.vcf -o /tmp/Uf6bgVvuEA/scatter.1.3 -s 21,22 -x X && cd /tmp/Uf6bgVvuEA/scatter.1.3 && cat 21.vcf 22.vcf X.vcf | grep -v ^##
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version   /tmp/Uf6bgVvuEA/concat.1.a.vcf.gz /tmp/Uf6bgVvuEA/concat.1.b.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob   /tmp/Uf6bgVvuEA/concat.1.a.vcf.gz /tmp/Uf6bgVvuEA/concat.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version   /tmp/Uf6bgVvuEA/concat.1.a.bcf /tmp/Uf6bgVvuEA/concat.1.b.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob   /tmp/Uf6bgVvuEA/concat.1.a.bcf /tmp/Uf6bgVvuEA/concat.1.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version -a  /tmp/Uf6bgVvuEA/concat.2.a.vcf.gz /tmp/Uf6bgVvuEA/concat.2.b.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob -a  /tmp/Uf6bgVvuEA/concat.2.a.vcf.gz /tmp/Uf6bgVvuEA/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version -a  /tmp/Uf6bgVvuEA/concat.2.a.bcf /tmp/Uf6bgVvuEA/concat.2.b.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob -a  /tmp/Uf6bgVvuEA/concat.2.a.bcf /tmp/Uf6bgVvuEA/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version -aD  /tmp/Uf6bgVvuEA/concat.2.a.vcf.gz /tmp/Uf6bgVvuEA/concat.2.b.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob -aD  /tmp/Uf6bgVvuEA/concat.2.a.vcf.gz /tmp/Uf6bgVvuEA/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version -aD  /tmp/Uf6bgVvuEA/concat.2.a.bcf /tmp/Uf6bgVvuEA/concat.2.b.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob -aD  /tmp/Uf6bgVvuEA/concat.2.a.bcf /tmp/Uf6bgVvuEA/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version -l --ligate-warn  /tmp/Uf6bgVvuEA/concat.3.a.vcf.gz /tmp/Uf6bgVvuEA/concat.3.b.vcf.gz /tmp/Uf6bgVvuEA/concat.3.0.vcf.gz /tmp/Uf6bgVvuEA/concat.3.c.vcf.gz /tmp/Uf6bgVvuEA/concat.3.d.vcf.gz /tmp/Uf6bgVvuEA/concat.3.e.vcf.gz /tmp/Uf6bgVvuEA/concat.3.f.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob -l --ligate-warn  /tmp/Uf6bgVvuEA/concat.3.a.vcf.gz /tmp/Uf6bgVvuEA/concat.3.b.vcf.gz /tmp/Uf6bgVvuEA/concat.3.0.vcf.gz /tmp/Uf6bgVvuEA/concat.3.c.vcf.gz /tmp/Uf6bgVvuEA/concat.3.d.vcf.gz /tmp/Uf6bgVvuEA/concat.3.e.vcf.gz /tmp/Uf6bgVvuEA/concat.3.f.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version -l --ligate-warn  /tmp/Uf6bgVvuEA/concat.3.a.bcf /tmp/Uf6bgVvuEA/concat.3.b.bcf /tmp/Uf6bgVvuEA/concat.3.0.bcf /tmp/Uf6bgVvuEA/concat.3.c.bcf /tmp/Uf6bgVvuEA/concat.3.d.bcf /tmp/Uf6bgVvuEA/concat.3.e.bcf /tmp/Uf6bgVvuEA/concat.3.f.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob -l --ligate-warn  /tmp/Uf6bgVvuEA/concat.3.a.bcf /tmp/Uf6bgVvuEA/concat.3.b.bcf /tmp/Uf6bgVvuEA/concat.3.0.bcf /tmp/Uf6bgVvuEA/concat.3.c.bcf /tmp/Uf6bgVvuEA/concat.3.d.bcf /tmp/Uf6bgVvuEA/concat.3.e.bcf /tmp/Uf6bgVvuEA/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
Random seed for test_naive_concat: 303452074
.. ok

test_naive_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --naive-force /tmp/Uf6bgVvuEA/naive_concat.0.bcf /tmp/Uf6bgVvuEA/naive_concat.1.bcf /tmp/Uf6bgVvuEA/naive_concat.2.bcf /tmp/Uf6bgVvuEA/naive_concat.3.bcf /tmp/Uf6bgVvuEA/naive_concat.4.bcf /tmp/Uf6bgVvuEA/naive_concat.5.bcf /tmp/Uf6bgVvuEA/naive_concat.6.bcf /tmp/Uf6bgVvuEA/naive_concat.7.bcf /tmp/Uf6bgVvuEA/naive_concat.8.bcf /tmp/Uf6bgVvuEA/naive_concat.9.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view -H
.. ok

test_naive_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --naive /tmp/Uf6bgVvuEA/naive_concat.0.vcf.gz /tmp/Uf6bgVvuEA/naive_concat.1.vcf.gz /tmp/Uf6bgVvuEA/naive_concat.2.vcf.gz /tmp/Uf6bgVvuEA/naive_concat.3.vcf.gz /tmp/Uf6bgVvuEA/naive_concat.4.vcf.gz /tmp/Uf6bgVvuEA/naive_concat.5.vcf.gz /tmp/Uf6bgVvuEA/naive_concat.6.vcf.gz /tmp/Uf6bgVvuEA/naive_concat.7.vcf.gz /tmp/Uf6bgVvuEA/naive_concat.8.vcf.gz /tmp/Uf6bgVvuEA/naive_concat.9.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view -H
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version -l  /tmp/Uf6bgVvuEA/concat.4.a.vcf.gz /tmp/Uf6bgVvuEA/concat.4.b.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob -l  /tmp/Uf6bgVvuEA/concat.4.a.vcf.gz /tmp/Uf6bgVvuEA/concat.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version -l  /tmp/Uf6bgVvuEA/concat.4.a.bcf /tmp/Uf6bgVvuEA/concat.4.b.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob -l  /tmp/Uf6bgVvuEA/concat.4.a.bcf /tmp/Uf6bgVvuEA/concat.4.b.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version -l --ligate-warn  /tmp/Uf6bgVvuEA/concat.5.a.vcf.gz /tmp/Uf6bgVvuEA/concat.5.b.vcf.gz /tmp/Uf6bgVvuEA/concat.5.c.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob -l --ligate-warn  /tmp/Uf6bgVvuEA/concat.5.a.vcf.gz /tmp/Uf6bgVvuEA/concat.5.b.vcf.gz /tmp/Uf6bgVvuEA/concat.5.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version -l --ligate-warn  /tmp/Uf6bgVvuEA/concat.5.a.bcf /tmp/Uf6bgVvuEA/concat.5.b.bcf /tmp/Uf6bgVvuEA/concat.5.c.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob -l --ligate-warn  /tmp/Uf6bgVvuEA/concat.5.a.bcf /tmp/Uf6bgVvuEA/concat.5.b.bcf /tmp/Uf6bgVvuEA/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version -l --ligate-force  /tmp/Uf6bgVvuEA/concat.5.a.bcf /tmp/Uf6bgVvuEA/concat.5.b.bcf /tmp/Uf6bgVvuEA/concat.5.c.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob -l --ligate-force  /tmp/Uf6bgVvuEA/concat.5.a.bcf /tmp/Uf6bgVvuEA/concat.5.b.bcf /tmp/Uf6bgVvuEA/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version -G -a -D  /tmp/Uf6bgVvuEA/concat.5.a.vcf.gz /tmp/Uf6bgVvuEA/concat.5.b.vcf.gz /tmp/Uf6bgVvuEA/concat.5.c.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob -G -a -D  /tmp/Uf6bgVvuEA/concat.5.a.vcf.gz /tmp/Uf6bgVvuEA/concat.5.b.vcf.gz /tmp/Uf6bgVvuEA/concat.5.c.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat --no-version -G -a -D  /tmp/Uf6bgVvuEA/concat.5.a.bcf /tmp/Uf6bgVvuEA/concat.5.b.bcf /tmp/Uf6bgVvuEA/concat.5.c.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.20/bcftools concat -Ob -G -a -D  /tmp/Uf6bgVvuEA/concat.5.a.bcf /tmp/Uf6bgVvuEA/concat.5.b.bcf /tmp/Uf6bgVvuEA/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.hdr /builddir/build/BUILD/bcftools-1.20/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.20/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.hdr /tmp/Uf6bgVvuEA/reheader.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/Uf6bgVvuEA/reheader.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.hdr /tmp/Uf6bgVvuEA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/Uf6bgVvuEA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples /builddir/build/BUILD/bcftools-1.20/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.20/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples /tmp/Uf6bgVvuEA/reheader.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/Uf6bgVvuEA/reheader.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples /tmp/Uf6bgVvuEA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/Uf6bgVvuEA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples2 /builddir/build/BUILD/bcftools-1.20/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.20/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples2 /tmp/Uf6bgVvuEA/reheader.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/Uf6bgVvuEA/reheader.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples2 /tmp/Uf6bgVvuEA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/Uf6bgVvuEA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples3 /builddir/build/BUILD/bcftools-1.20/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.20/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples3 /tmp/Uf6bgVvuEA/reheader.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/Uf6bgVvuEA/reheader.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples3 /tmp/Uf6bgVvuEA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/Uf6bgVvuEA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples4 /builddir/build/BUILD/bcftools-1.20/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.20/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples4 /tmp/Uf6bgVvuEA/reheader.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/Uf6bgVvuEA/reheader.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples4 /tmp/Uf6bgVvuEA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/Uf6bgVvuEA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -s /builddir/build/BUILD/bcftools-1.20/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.empty.hdr /builddir/build/BUILD/bcftools-1.20/test/empty.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.20/test/empty.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.empty.hdr /tmp/Uf6bgVvuEA/empty.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/Uf6bgVvuEA/empty.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.empty.hdr /tmp/Uf6bgVvuEA/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/Uf6bgVvuEA/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -f /builddir/build/BUILD/bcftools-1.20/test/reheader.fai /builddir/build/BUILD/bcftools-1.20/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -f /builddir/build/BUILD/bcftools-1.20/test/reheader.fai /tmp/Uf6bgVvuEA/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -f /builddir/build/BUILD/bcftools-1.20/test/reheader.fai /tmp/Uf6bgVvuEA/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.20/test/reheader.fai /builddir/build/BUILD/bcftools-1.20/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.20/test/reheader.fai /tmp/Uf6bgVvuEA/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -h /builddir/build/BUILD/bcftools-1.20/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.20/test/reheader.fai /tmp/Uf6bgVvuEA/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -f /builddir/build/BUILD/bcftools-1.20/test/reheader.3.fai /builddir/build/BUILD/bcftools-1.20/test/reheader.3.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -f /builddir/build/BUILD/bcftools-1.20/test/reheader.3.fai /tmp/Uf6bgVvuEA/reheader.3.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.20/bcftools reheader -f /builddir/build/BUILD/bcftools-1.20/test/reheader.3.fai /tmp/Uf6bgVvuEA/reheader.3.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools view --no-version
.. ok

test_rename_chrs:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate --rename-chrs /tmp/Uf6bgVvuEA/rename.map -Ov /tmp/Uf6bgVvuEA/annotate.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM\t%POS\n'
.. ok

test_rename_chrs:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate --rename-chrs /tmp/Uf6bgVvuEA/rename.map -Ob /tmp/Uf6bgVvuEA/annotate.bcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM\t%POS\n'
.. ok

test_rename_chrs:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate --rename-chrs /tmp/Uf6bgVvuEA/rename.map -Ov /builddir/build/BUILD/bcftools-1.20/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM\t%POS\n'
.. ok

test_rename_chrs:
	/builddir/build/BUILD/bcftools-1.20/bcftools annotate --rename-chrs /tmp/Uf6bgVvuEA/rename.map -Ob /builddir/build/BUILD/bcftools-1.20/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%CHROM\t%POS\n'
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,. /tmp/Uf6bgVvuEA/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,.
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,. --vcf-ids /tmp/Uf6bgVvuEA/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,. --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,. --vcf-ids --3N6 /tmp/Uf6bgVvuEA/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,. --vcf-ids --3N6
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -g .,- /tmp/Uf6bgVvuEA/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -g .,-
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert  --vcf-ids -G /builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert  --vcf-ids -G /builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -G /builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -G /builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -G /builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -G /builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.20/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,. --tag PL /tmp/Uf6bgVvuEA/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,. --tag PL
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -g .,- --tag PL /tmp/Uf6bgVvuEA/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -g .,- --tag PL
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,. --vcf-ids /tmp/Uf6bgVvuEA/check.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/check.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,. --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -g .,- --vcf-ids /tmp/Uf6bgVvuEA/check.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/check.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -g .,- --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,. --3N6 /tmp/Uf6bgVvuEA/check.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/check.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,. --3N6
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -g .,- --3N6 /tmp/Uf6bgVvuEA/check.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/check.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -g .,- --3N6
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,. --3N6 --vcf-ids /tmp/Uf6bgVvuEA/check.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/check.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -g -,. --3N6 --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -g .,- --3N6 --vcf-ids /tmp/Uf6bgVvuEA/check.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/check.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -g .,- --3N6 --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -h -,.,. /tmp/Uf6bgVvuEA/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -h -,.,.
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -h .,-,. /tmp/Uf6bgVvuEA/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -h .,-,.
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -h .,-,. --vcf-ids /tmp/Uf6bgVvuEA/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -h .,-,. --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -h .,.,- /tmp/Uf6bgVvuEA/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert -h .,.,-
.. ok

test_vcf_convert_hls2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -H /builddir/build/BUILD/bcftools-1.20/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.20/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.20/test/convert.hls.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hls2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -H /builddir/build/BUILD/bcftools-1.20/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.20/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.20/test/convert.hls.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --haplegendsample -,.,. /tmp/Uf6bgVvuEA/convert.hap-missing.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.hap-missing.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert --haplegendsample -,.,.
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --hapsample -,. /tmp/Uf6bgVvuEA/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert --hapsample -,.
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --hapsample -,. --vcf-ids /tmp/Uf6bgVvuEA/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert --hapsample -,. --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --hapsample .,- /tmp/Uf6bgVvuEA/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert --hapsample .,-
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.20/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.20/test/convert.hs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.20/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.20/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.20/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.20/test/convert.hs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.20/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.20/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##
.. ok

test_vcf_convert_gvcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa /tmp/Uf6bgVvuEA/convert.gvcf.vcf.gz
.. ok

test_vcf_convert_gvcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools view -Ob /tmp/Uf6bgVvuEA/convert.gvcf.vcf.gz | /builddir/build/BUILD/bcftools-1.20/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.20/test/gvcf.fa | grep -v ^##bcftools
.. ok

test_vcf_convert_tsv2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --no-version  -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.20/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.20/test/convert.23andme
.. ok

test_vcf_convert_tsv2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -Ou  -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.20/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.20/test/convert.23andme | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_convert_tsv2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert --no-version  -c -,CHROM,POS,REF,ALT -f /builddir/build/BUILD/bcftools-1.20/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.20/test/convert.tsv
.. ok

test_vcf_convert_tsv2vcf:
	/builddir/build/BUILD/bcftools-1.20/bcftools convert -Ou  -c -,CHROM,POS,REF,ALT -f /builddir/build/BUILD/bcftools-1.20/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.20/test/convert.tsv | /builddir/build/BUILD/bcftools-1.20/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -m /builddir/build/BUILD/bcftools-1.20/test/consensus.tab 
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -m /builddir/build/BUILD/bcftools-1.20/test/consensus.tab 
.. ok

test_vcf_consensus_chain:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -m /builddir/build/BUILD/bcftools-1.20/test/consensus.tab -c /tmp/Uf6bgVvuEA/consensus.1.chain.new >/dev/null; cat /tmp/Uf6bgVvuEA/consensus.1.chain.new
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.20/test/consensus.tab 
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.20/test/consensus.tab 
.. ok

test_vcf_consensus_chain:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.20/test/consensus.tab -c /tmp/Uf6bgVvuEA/consensus.2.chain.new >/dev/null; cat /tmp/Uf6bgVvuEA/consensus.2.chain.new
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -I -s - -m /builddir/build/BUILD/bcftools-1.20/test/consensus.tab 
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -I -s - -m /builddir/build/BUILD/bcftools-1.20/test/consensus.tab 
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -I -m /builddir/build/BUILD/bcftools-1.20/test/consensus.tab --mask-with X -m /builddir/build/BUILD/bcftools-1.20/test/consensus.tab --mask-with lc  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -I -m /builddir/build/BUILD/bcftools-1.20/test/consensus.tab --mask-with X -m /builddir/build/BUILD/bcftools-1.20/test/consensus.tab --mask-with lc  
.. ok

test_vcf_consensus_chain:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.20/test/consensus.tab -c /tmp/Uf6bgVvuEA/consensus.3.chain.new >/dev/null; cat /tmp/Uf6bgVvuEA/consensus.3.chain.new
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -H 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -H 1  
.. ok

test_vcf_consensus_chain:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -H 1  -c /tmp/Uf6bgVvuEA/consensus.4.chain.new >/dev/null; cat /tmp/Uf6bgVvuEA/consensus.4.chain.new
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus2.fa -H 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus2.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus2.fa -H 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus2.fa -H 2  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus2.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus2.fa -H 2  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/empty.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/empty.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus2.fa -H 2 -M "?"  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus3.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus2.fa -H 2 -M "?"  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus2.fa -H 2 -M "?" -p xx_  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus3.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus2.fa -H 2 -M "?" -p xx_  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus4.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus2.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus4.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus2.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus5.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus5.fa --haplotype LA  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus5.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus5.fa --haplotype LA  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus6.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus6.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus6.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus6.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 2  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 2  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 4  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 4  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 2pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 2pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 4pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 4pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 3  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 3  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 1pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 1pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 3pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus7.fa -H 3pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus8.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -a .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus8.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -a .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus8.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -a . -i 'ALT!="<DEL>"'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus8.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -a . -i 'ALT!="<DEL>"'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -a . -e 'MinDP>15'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus8.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -a . -e 'MinDP>15'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -a . -e 'MinDP<15'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus8.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -a . -e 'MinDP<15'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.9.1.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.9.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.9.1.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.9.2.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.9.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.9.2.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.9.1.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.10.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.9.1.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.9.2.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.10.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.9.2.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.11.fa -s smpl  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.11.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.11.fa -s smpl  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.11.fa -s smpl -a N  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.11.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.11.fa -s smpl -a N  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.12.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.12.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.12.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.13.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.13.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.13.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.13.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.14.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.14.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.14.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.14.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.12.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv :  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.12.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv :  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.15.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.15.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -I  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.16.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -s - -I  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -H I  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.16.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.fa -H I  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.17.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus2.fa -s - -M N -m /builddir/build/BUILD/bcftools-1.20/test/consensus.17.bed 
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.17.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus2.fa -s - -M N -m /builddir/build/BUILD/bcftools-1.20/test/consensus.17.bed 
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.18.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.18.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.18.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.18.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.19.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.19.fa -s -   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.19.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.19.fa -s -   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.20.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.20.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.20.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.20.fa   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.20.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.20.fa   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.20.fa -M . -s b  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.20.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.20.fa -M . -s b  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.20.fa -M . -s a  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.20.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.20.fa -M . -s a  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.21.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.21.fa   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.21.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.21.fa   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.22.fa --regions-overlap 0 --mark-del .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.22.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.22.fa --regions-overlap 0 --mark-del .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.22.fa --regions-overlap 1 --mark-del .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.22.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.22.fa --regions-overlap 1 --mark-del .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.22.fa --regions-overlap 2 --mark-del .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.22.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.22.fa --regions-overlap 2 --mark-del .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.22.fa --regions-overlap 0  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.22.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.22.fa --regions-overlap 0  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.22.fa --regions-overlap 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.22.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.22.fa --regions-overlap 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.20/test/consensus.22.fa --regions-overlap 2  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.20/bcftools consensus /tmp/Uf6bgVvuEA/consensus.22.bcf    -f /builddir/build/BUILD/bcftools-1.20/test/consensus.22.fa --regions-overlap 2  
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -b /tmp/Uf6bgVvuEA/mpileup.bam.list --no-version | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob -b /tmp/Uf6bgVvuEA/mpileup.bam.urllist | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -b /tmp/Uf6bgVvuEA/mpileup.cram.list --no-version | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob -b /tmp/Uf6bgVvuEA/mpileup.cram.urllist | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.20/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.20/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.20/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.20/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.20/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.20/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.20/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.20/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.20/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.20/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.20/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.20/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.20/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.20/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.20/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.20/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.20/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.20/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.20/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.20/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup  -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup  -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup  -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup  -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup  -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup  -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.20/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.20/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.20/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.20/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.20/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.20/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.20/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.20/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.20/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.20/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.20/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.20/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.sam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.sam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.1.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.cram | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.1.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.1.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.1.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.2.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.2.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.2.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.3.fa /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.3.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.3.fa -Ob /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.3.1.bam /builddir/build/BUILD/bcftools-1.20/test/mpileup/annot-NMBZ.3.2.bam | /builddir/build/BUILD/bcftools-1.20/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq.gff3 /builddir/build/BUILD/bcftools-1.20/test/csq.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq.chr.gff3 /builddir/build/BUILD/bcftools-1.20/test/csq.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq.2.gff /builddir/build/BUILD/bcftools-1.20/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq.2.gff --ncsq 64 /builddir/build/BUILD/bcftools-1.20/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq.nchr.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq.nchr.gff /builddir/build/BUILD/bcftools-1.20/test/csq.nchr.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq.ychr.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq.nchr.gff /builddir/build/BUILD/bcftools-1.20/test/csq.nchr.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq.nchr.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq.ychr.gff /builddir/build/BUILD/bcftools-1.20/test/csq.nchr.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq.ychr.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq.ychr.gff /builddir/build/BUILD/bcftools-1.20/test/csq.nchr.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq.ychr.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq.ychr.gff /builddir/build/BUILD/bcftools-1.20/test/csq.ychr.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq.ychr.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq.nchr.gff /builddir/build/BUILD/bcftools-1.20/test/csq.ychr.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq.nchr.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq.ychr.gff /builddir/build/BUILD/bcftools-1.20/test/csq.ychr.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq.nchr.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq.nchr.gff /builddir/build/BUILD/bcftools-1.20/test/csq.ychr.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000263103-INS/insertions.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000000000 && /builddir/build/BUILD/bcftools-1.20/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf  | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000413103/ENST00000413103.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000413103/ENST00000413103.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000413103/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENSG00000173376/ENSG00000173376.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENSG00000173376/ENSG00000173376.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENSG00000173376/synon.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000448695/ENST00000448695.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000448695/ENST00000448695.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000368801/ENST00000368801.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000368801/ENST00000368801.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000368801/compound-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000520868/ENST00000520868.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000520868/ENST00000520868.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000520868/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000381157/ENST00000381157.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000381157/ENST00000381157.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000381157/haploid-diploid.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000420670/segfault.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000420670/start-stop-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000545279/ENST00000545279.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000545279/ENST00000545279.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000545279/splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000218032/start-lost-del.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000409523/ENST00000409523.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000409523/ENST00000409523.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000409523/long-overlapping-del.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000360372/ENST00000360372.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000360372/ENST00000360372.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000360372/mnp.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000410009/ENST00000410009.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000410009/ENST00000410009.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000410009/frameshift.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.20/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.20/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.20/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000624631/ENST00000624631.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000624631/ENST00000624631.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000624631/ambiguous.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000227471/ENST00000227471.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000227471/ENST00000227471.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000256452/ENST00000256452.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000256452/ENST00000256452.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000256452/intron.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000271583/ENST00000271583.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000271583/ENST00000271583.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000271583/splice-acceptor.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000269081/ENST00000269081.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000269081/ENST00000269081.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/EDUMMY0002/EDUMMY0002.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/EDUMMY0002/EDUMMY0002.gff /builddir/build/BUILD/bcftools-1.20/test/csq/EDUMMY0002/boundaries.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.20/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.20/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.20/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000318249.2/ENST00000318249.2.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000375992/ENST00000375992.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000375992/ENST00000375992.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000436063/ENST00000436063.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000436063/ENST00000436063.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000436063/insert-before-utr.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.20/test/csq/ENSMUST00000133836 && /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/EDUMMY0003/EDUMMY0003.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/EDUMMY0003/EDUMMY0003.gff /builddir/build/BUILD/bcftools-1.20/test/csq/EDUMMY0003/long-del.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000557788/ENST00000557788.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000557788/ENST00000557788.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000557788/long-overlap-del.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000420190/ENST00000420190.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000420190/ENST00000420190.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000420190/abort-in-csq-push.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000519442/ENST00000519442.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000519442/ENST00000519442.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000519442/synon-splice-region-del.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000580206 && /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000400151/ENST00000400151.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000400151/ENST00000400151.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000400151/long-del.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.20/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.20/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000382647/ENST00000382647.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000382647/ENST00000382647.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000518414/ENST00000518414.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000518414/ENST00000518414.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000368801.2/ENST00000368801.2.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000368801.2/start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000230048/ENST00000230048.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000230048/ENST00000230048.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000230048/start-del.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000357367/ENST00000357367.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000357367/ENST00000357367.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000357367/stop-retained.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000285021/ENST00000285021.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000285021/ENST00000285021.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000571540/ENST00000571540.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000571540/ENST00000571540.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000571540/nmd.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000301246/ENST00000301246.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000301246/ENST00000301246.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000301246/15bp-insert.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000379416 && /builddir/build/BUILD/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf       | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf       | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf       | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf       | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf                 | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.20/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.20/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.20/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.20/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000390520/ENST00000390520.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000390520/ENST00000390520.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000390520/deletion-overlap.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000422159 && /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf  | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /builddir/build/BUILD/bcftools-1.20/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000528237/ENST00000528237.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000528237/ENST00000528237.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000593942/ENST00000593942.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000593942/ENST00000593942.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000593942/last-codon-deletion.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.20/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.20/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.20/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.20/bcftools roh /builddir/build/BUILD/bcftools-1.20/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^#
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.20/bcftools roh /builddir/build/BUILD/bcftools-1.20/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.20/test/roh.1.tab.gz| grep -v ^#
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.20/bcftools roh /builddir/build/BUILD/bcftools-1.20/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.20/test/roh.1.tab.gz --ignore-homref| grep -v ^#
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.20/bcftools roh /builddir/build/BUILD/bcftools-1.20/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^#
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.20/bcftools roh /builddir/build/BUILD/bcftools-1.20/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^#
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.20/bcftools roh /builddir/build/BUILD/bcftools-1.20/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^#
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.20/bcftools roh /builddir/build/BUILD/bcftools-1.20/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^#
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 /tmp/Uf6bgVvuEA/gtcheck.1.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -u GT,GT /tmp/Uf6bgVvuEA/gtcheck.1.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -u GT,PL /tmp/Uf6bgVvuEA/gtcheck.1.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -u PL,GT /tmp/Uf6bgVvuEA/gtcheck.1.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -u PL,PL /tmp/Uf6bgVvuEA/gtcheck.1.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -p s1,s1 /tmp/Uf6bgVvuEA/gtcheck.1.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 /tmp/Uf6bgVvuEA/gtcheck.2.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0  /tmp/Uf6bgVvuEA/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/Uf6bgVvuEA/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.20/test/gtcheck.3.pairs /tmp/Uf6bgVvuEA/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -u PL /tmp/Uf6bgVvuEA/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 --n-matches 4 /tmp/Uf6bgVvuEA/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO  | sort
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/Uf6bgVvuEA/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/Uf6bgVvuEA/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/Uf6bgVvuEA/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/Uf6bgVvuEA/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/Uf6bgVvuEA/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -p B,C,B,D /tmp/Uf6bgVvuEA/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -u GT,GT -H /tmp/Uf6bgVvuEA/gtcheck.1.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -u GT,PL -H /tmp/Uf6bgVvuEA/gtcheck.1.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -u PL,GT -H /tmp/Uf6bgVvuEA/gtcheck.1.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -u PL,PL -H /tmp/Uf6bgVvuEA/gtcheck.1.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.20/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/Uf6bgVvuEA/gtcheck.4.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.20/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/Uf6bgVvuEA/gtcheck.4.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -u GT -e 30 /tmp/Uf6bgVvuEA/gtcheck.1.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/Uf6bgVvuEA/gtcheck.1.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -u GT -e 300 /tmp/Uf6bgVvuEA/gtcheck.1.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -u PL -e 30 /tmp/Uf6bgVvuEA/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck  /tmp/Uf6bgVvuEA/gtcheck.ntop.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck --n-matches 2 /tmp/Uf6bgVvuEA/gtcheck.ntop.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck  /tmp/Uf6bgVvuEA/gtcheck.5.vcf.gz -g /tmp/Uf6bgVvuEA/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -p A,B,B,C /tmp/Uf6bgVvuEA/gtcheck.6.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.20/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/Uf6bgVvuEA/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok


Number of tests:
    total   .. 2129
    passed  .. 2129
    failed  .. 0

+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: bcftools-1.20-1.el9.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.TGXcaW
+ umask 022
+ cd /builddir/build/BUILD
+ cd bcftools-1.20
+ DOCDIR=/builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/share/doc/bcftools
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/share/doc/bcftools
+ cp -pr AUTHORS /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/share/doc/bcftools
+ cp -pr NEWS /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/share/doc/bcftools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.GoxNF4
+ umask 022
+ cd /builddir/build/BUILD
+ cd bcftools-1.20
+ LICENSEDIR=/builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/share/licenses/bcftools
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/share/licenses/bcftools
+ cp -pr LICENSE /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64/usr/share/licenses/bcftools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: bcftools = 1.20-1.el9 bcftools(x86-64) = 1.20-1.el9
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl /usr/bin/python3 libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libgsl.so.25()(64bit) libgslcblas.so.0()(64bit) libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(64bit) libhts.so.3(HTSLIB_1.1)(64bit) libhts.so.3(HTSLIB_1.10)(64bit) libhts.so.3(HTSLIB_1.13)(64bit) libhts.so.3(HTSLIB_1.16)(64bit) libhts.so.3(HTSLIB_1.17)(64bit) libhts.so.3(HTSLIB_1.2.1)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.6)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libperl.so.5.32()(64bit) rtld(GNU_HASH)
Conflicts: samtools < 1.0
Processing files: bcftools-debugsource-1.20-1.el9.x86_64
Provides: bcftools-debugsource = 1.20-1.el9 bcftools-debugsource(x86-64) = 1.20-1.el9
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: bcftools-debuginfo-1.20-1.el9.x86_64
Provides: bcftools-debuginfo = 1.20-1.el9 bcftools-debuginfo(x86-64) = 1.20-1.el9 debuginfo(build-id) = 00a15b1153ea4d45dfa846e0369e644f0793ed80 debuginfo(build-id) = 0188bffd74d42aa678269b3ccf2bf96db66841d2 debuginfo(build-id) = 021325933f319c7dd731ddc2aa0e9a2a61f18d92 debuginfo(build-id) = 09bfeeddb33c5eaaf5a648139f8292d132c1b27e debuginfo(build-id) = 0acf54253b9a973d0ad9f0f2d50a31c505d719f5 debuginfo(build-id) = 14d37784d1a6c9d2e2ba3dec11229b6a66e81232 debuginfo(build-id) = 220294a3801efa1b6c66a57374948cd02f1b024e debuginfo(build-id) = 22aa1052e8c27fc9fe00cee54b37c0c14f08095a debuginfo(build-id) = 22bb4c3066a6e3ad545b2ed244d33d492b394603 debuginfo(build-id) = 233db973ea35683bda6eb66d24e753c7b6319da2 debuginfo(build-id) = 2ada4123699fb4daf0153021629c1ea4de8bb4b2 debuginfo(build-id) = 2d986027d73e52e6d4fa16e5eac743808ba8845c debuginfo(build-id) = 353dea41fa015484ebe2608fab0baaa77730b4fc debuginfo(build-id) = 3d1d505fc7e305c64b41db31dcb5f01eef41280a debuginfo(build-id) = 407b2c8673600b786107cbf8a5f6cf2259c381d0 debuginfo(build-id) = 44a3b7eaa1f01e7dd183c6b10987656c617b5eda debuginfo(build-id) = 464398a8a6fd55e15635fcb45fcd01dcf4ac771a debuginfo(build-id) = 4a9a27a25c8d3acdb1ebee489552beba80be6769 debuginfo(build-id) = 4e48907b4bc502fb9c1de2354418ef0b4b3a7dcc debuginfo(build-id) = 4f3d44e6edb23a64d82be7cd4933f464cc0c9867 debuginfo(build-id) = 591e1022fbadf6d6912db7f073f7f038131bc2d4 debuginfo(build-id) = 5f5415cee4101ffdcab4406fd51b3c643ed44fb5 debuginfo(build-id) = 7233d43ef5c119a5c5099f1ef5ebcb754d3a2698 debuginfo(build-id) = 78ff1e7ea75b0e1ca94c725c2b4eb9f913cde307 debuginfo(build-id) = 7a7931bffb2e66c999fe42bf5f9d328d188b5ff1 debuginfo(build-id) = 824068a0cbef0bbc9e111c4dbbf4990a5afa3167 debuginfo(build-id) = badc1769da1ea21d21aa384e251585553b0b191c debuginfo(build-id) = bb484eb8c0248dbb79a02dfe07815c6f099f46b0 debuginfo(build-id) = c04131091826b62d940fc25911e7ca8db2ed9b97 debuginfo(build-id) = c473b7a05666005c3fad9c71dc7cf0cba99e7246 debuginfo(build-id) = cb70faacd2263914f603d9358e1898b7e29c2eb8 debuginfo(build-id) = ceb08fbc2bd076074978aa1018dde38fbc386ead debuginfo(build-id) = d1c8270d566bf0b8de15dcc725e3b9f8db39d6ac debuginfo(build-id) = d205262c732e8451c5f27545426ee6e66a26255a debuginfo(build-id) = d9e52c9719a4ac42eb964c51bc6f803210107852 debuginfo(build-id) = da652145e78da88925edd15bf40eb6df4333d89a debuginfo(build-id) = dcd21de486f3af834a7746599ff2d611ebe01473 debuginfo(build-id) = f3b987c69a92aeb1b1c4c2cb371460284aa2629a debuginfo(build-id) = f522dc433bd809019c287a762353f1a59f1a5445 debuginfo(build-id) = f9da1d851f4bb1ab053167e71a88b7cd935717ef
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: bcftools-debugsource(x86-64) = 1.20-1.el9
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64
Wrote: /builddir/build/RPMS/bcftools-debugsource-1.20-1.el9.x86_64.rpm
Wrote: /builddir/build/RPMS/bcftools-1.20-1.el9.x86_64.rpm
Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.20-1.el9.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Wy6Dbv
+ umask 022
+ cd /builddir/build/BUILD
+ cd bcftools-1.20
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/bcftools-1.20-1.el9.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild bcftools-1.20-1.el9.src.rpm
Finish: build phase for bcftools-1.20-1.el9.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/rhel+epel-9-x86_64-1717414005.411382/root/var/log/dnf.log
/var/lib/mock/rhel+epel-9-x86_64-1717414005.411382/root/var/log/dnf.librepo.log
/var/lib/mock/rhel+epel-9-x86_64-1717414005.411382/root/var/log/dnf.rpm.log
INFO: Done(/var/lib/copr-rpmbuild/results/bcftools-1.20-1.el9.src.rpm) Config(child) 2 minutes 14 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "bcftools",
            "epoch": null,
            "version": "1.20",
            "release": "1.el9",
            "arch": "x86_64"
        },
        {
            "name": "bcftools",
            "epoch": null,
            "version": "1.20",
            "release": "1.el9",
            "arch": "src"
        },
        {
            "name": "bcftools-debugsource",
            "epoch": null,
            "version": "1.20",
            "release": "1.el9",
            "arch": "x86_64"
        },
        {
            "name": "bcftools-debuginfo",
            "epoch": null,
            "version": "1.20",
            "release": "1.el9",
            "arch": "x86_64"
        }
    ]
}
RPMResults finished