Warning: Permanently added '107.23.229.86' (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/8069455-fedora-rawhide-aarch64 --chroot fedora-rawhide-aarch64
Version: 0.73
PID: 7382
Logging PID: 7383
Task:
{'allow_user_ssh': False,
'appstream': False,
'background': False,
'build_id': 8069455,
'buildroot_pkgs': [],
'chroot': 'fedora-rawhide-aarch64',
'enable_net': False,
'fedora_review': False,
'git_hash': '5e8f7a6461ef08091b670726100a86d9720b3c37',
'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ljavorsk/zlib-ng-rebase-fedora/bcftools',
'isolation': 'default',
'memory_reqs': 2048,
'package_name': 'bcftools',
'package_version': '1.15.1-10',
'project_dirname': 'zlib-ng-rebase-fedora',
'project_name': 'zlib-ng-rebase-fedora',
'project_owner': 'ljavorsk',
'repo_priority': None,
'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ljavorsk/zlib-ng-rebase-fedora/fedora-rawhide-aarch64/',
'id': 'copr_base',
'name': 'Copr repository',
'priority': None}],
'sandbox': 'ljavorsk/zlib-ng-rebase-fedora--ljavorsk',
'source_json': {},
'source_type': None,
'ssh_public_keys': None,
'submitter': 'ljavorsk',
'tags': [],
'task_id': '8069455-fedora-rawhide-aarch64',
'timeout': 18000,
'uses_devel_repo': False,
'with_opts': [],
'without_opts': []}
Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ljavorsk/zlib-ng-rebase-fedora/bcftools /var/lib/copr-rpmbuild/workspace/workdir-441cyqx1/bcftools --depth 500 --no-single-branch --recursive
cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ljavorsk/zlib-ng-rebase-fedora/bcftools', '/var/lib/copr-rpmbuild/workspace/workdir-441cyqx1/bcftools', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout:
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-441cyqx1/bcftools'...
Running: git checkout 5e8f7a6461ef08091b670726100a86d9720b3c37 --
cmd: ['git', 'checkout', '5e8f7a6461ef08091b670726100a86d9720b3c37', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-441cyqx1/bcftools
rc: 0
stdout:
stderr: Note: switching to '5e8f7a6461ef08091b670726100a86d9720b3c37'.
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 5e8f7a6 automatic import of bcftools
Running: copr-distgit-client sources
cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-441cyqx1/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-1.15.1.tar.bz2
INFO: Reading stdout from command: curl --help all
/usr/bin/tail: INFO: Calling: curl -H Pragma: -o bcftools-1.15.1.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/ljavorsk/zlib-ng-rebase-fedora/bcftools/bcftools-1.15.1.tar.bz2/md5/37e0cbdbcbeb844b8592f4a2acb2fe3f/bcftools-1.15.1.tar.bz2
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
/var/lib/copr-rpmbuild/main.log: file truncated
100 6755k 100 6755k 0 0 208M 0 --:--:-- --:--:-- --:--:-- 212M
INFO: Reading stdout from command: md5sum bcftools-1.15.1.tar.bz2
Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-441cyqx1/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-441cyqx1/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727274377.320064 -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-441cyqx1/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-441cyqx1/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727274377.320064 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
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-441cyqx1/bcftools/bcftools.spec) Config(fedora-rawhide-aarch64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.6
INFO: Mock Version: 5.6
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1727274377.320064/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide
INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide
INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1727274377.320064/root
INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture
INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount
INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/1811ac4ffde70d7a142f548fca08095e5cad67d5b02ca184b763d6c52a090186/merged
INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/1811ac4ffde70d7a142f548fca08095e5cad67d5b02ca184b763d6c52a090186/merged) with podman image umount
INFO: Package manager dnf5 detected and used (fallback)
INFO: Not updating bootstrap chroot, bootstrap_image_ready=True
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-1727274377.320064/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 dnf5 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
rpm-4.19.94-1.fc42.aarch64
rpm-sequoia-1.7.0-2.fc41.aarch64
dnf5-5.2.6.2-1.fc42.aarch64
dnf5-plugins-5.2.6.2-1.fc42.aarch64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
fedora 100% | 36.2 MiB/s | 20.8 MiB | 00m01s
Copr repository 100% | 15.9 MiB/s | 584.9 KiB | 00m00s
Repositories loaded.
Package Arch Version Repository Size
Installing group/module packages:
bash aarch64 5.2.32-2.fc42 fedora 8.3 MiB
bzip2 aarch64 1.0.8-19.fc41 fedora 427.6 KiB
coreutils aarch64 9.5-9.fc42 fedora 20.8 MiB
cpio aarch64 2.15-2.fc41 fedora 1.2 MiB
diffutils aarch64 3.10-8.fc41 fedora 2.1 MiB
fedora-release-common noarch 42-0.3 fedora 19.4 KiB
findutils aarch64 1:4.10.0-4.fc41 fedora 2.1 MiB
gawk aarch64 5.3.0-4.fc41 fedora 4.2 MiB
glibc-minimal-langpack aarch64 2.40.9000-1.fc42 fedora 0.0 B
grep aarch64 3.11-9.fc41 fedora 1.1 MiB
gzip aarch64 1.13-2.fc41 fedora 488.9 KiB
info aarch64 7.1.1-1.fc42 fedora 613.6 KiB
patch aarch64 2.7.6-25.fc41 fedora 390.6 KiB
redhat-rpm-config noarch 295-1.fc42 fedora 186.6 KiB
rpm-build aarch64 4.19.94-1.fc42 fedora 1.4 MiB
sed aarch64 4.9-3.fc41 fedora 1.0 MiB
shadow-utils aarch64 2:4.16.0-4.fc42 fedora 7.3 MiB
tar aarch64 2:1.35-4.fc41 fedora 3.1 MiB
unzip aarch64 6.0-64.fc41 fedora 726.7 KiB
util-linux aarch64 2.40.2-8.fc42 fedora 16.9 MiB
which aarch64 2.21-42.fc41 fedora 248.2 KiB
xz aarch64 1:5.6.2-2.fc41 fedora 1.5 MiB
Installing dependencies:
add-determinism aarch64 0.3.6-1.fc41 fedora 2.0 MiB
alternatives aarch64 1.30-1.fc41 fedora 218.3 KiB
ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB
audit-libs aarch64 4.0.2-1.fc41 fedora 547.4 KiB
authselect aarch64 1.5.0-7.fc41 fedora 309.5 KiB
authselect-libs aarch64 1.5.0-7.fc41 fedora 931.9 KiB
basesystem noarch 11-21.fc41 fedora 0.0 B
binutils aarch64 2.43.50-1.fc42 copr_base 32.7 MiB
build-reproducibility-srpm-macros noarch 0.3.6-1.fc41 fedora 735.0 B
bzip2-libs aarch64 1.0.8-19.fc41 fedora 200.7 KiB
ca-certificates noarch 2024.2.69_v8.0.401-1.fc42 fedora 2.6 MiB
coreutils-common aarch64 9.5-9.fc42 fedora 11.2 MiB
cracklib aarch64 2.9.11-6.fc41 fedora 935.0 KiB
crypto-policies noarch 20240828-1.git5f66e81.fc42 fedora 136.9 KiB
curl aarch64 8.10.1-1.fc42 fedora 581.3 KiB
cyrus-sasl-lib aarch64 2.1.28-27.fc41 fedora 3.1 MiB
debugedit aarch64 5.0-17.fc41 fedora 499.2 KiB
dwz aarch64 0.15-7.fc41 fedora 386.8 KiB
ed aarch64 1.20.2-2.fc41 fedora 282.8 KiB
efi-srpm-macros noarch 5-12.fc41 fedora 40.1 KiB
elfutils aarch64 0.191-8.fc41 fedora 4.9 MiB
elfutils-debuginfod-client aarch64 0.191-8.fc41 fedora 396.9 KiB
elfutils-default-yama-scope noarch 0.191-8.fc41 fedora 1.8 KiB
elfutils-libelf aarch64 0.191-8.fc41 fedora 1.3 MiB
elfutils-libs aarch64 0.191-8.fc41 fedora 938.3 KiB
fedora-gpg-keys noarch 42-0.2 fedora 126.4 KiB
fedora-release noarch 42-0.3 fedora 0.0 B
fedora-release-identity-basic noarch 42-0.3 fedora 694.0 B
fedora-repos noarch 42-0.2 fedora 4.9 KiB
fedora-repos-rawhide noarch 42-0.2 fedora 2.2 KiB
file aarch64 5.45-7.fc41 fedora 267.5 KiB
file-libs aarch64 5.45-7.fc41 fedora 10.0 MiB
filesystem aarch64 3.18-29.fc42 fedora 106.0 B
fonts-srpm-macros noarch 1:2.0.5-17.fc41 fedora 55.8 KiB
forge-srpm-macros noarch 0.3.2-1.fc41 fedora 39.0 KiB
fpc-srpm-macros noarch 1.3-13.fc41 fedora 144.0 B
gdb-minimal aarch64 15.1-2.fc42 fedora 13.0 MiB
gdbm aarch64 1:1.23-7.fc41 fedora 928.5 KiB
gdbm-libs aarch64 1:1.23-7.fc41 fedora 426.0 KiB
ghc-srpm-macros noarch 1.9.2-1.fc42 fedora 779.0 B
glibc aarch64 2.40.9000-1.fc42 fedora 9.2 MiB
glibc-common aarch64 2.40.9000-1.fc42 fedora 2.6 MiB
glibc-gconv-extra aarch64 2.40.9000-1.fc42 fedora 49.2 MiB
gmp aarch64 1:6.3.0-2.fc41 fedora 722.0 KiB
gnat-srpm-macros noarch 6-6.fc41 fedora 1.0 KiB
go-srpm-macros noarch 3.6.0-3.fc41 fedora 60.8 KiB
jansson aarch64 2.13.1-10.fc41 fedora 220.5 KiB
kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB
keyutils-libs aarch64 1.6.3-4.fc41 fedora 226.4 KiB
krb5-libs aarch64 1.21.3-2.fc41 fedora 3.3 MiB
libacl aarch64 2.3.2-2.fc41 fedora 196.1 KiB
libarchive aarch64 3.7.6-1.fc42 fedora 974.8 KiB
libattr aarch64 2.5.2-4.fc41 fedora 196.6 KiB
libblkid aarch64 2.40.2-8.fc42 fedora 418.6 KiB
libbrotli aarch64 1.1.0-5.fc41 fedora 1.1 MiB
libcap aarch64 2.70-4.fc41 fedora 1.4 MiB
libcap-ng aarch64 0.8.5-3.fc41 fedora 417.2 KiB
libcom_err aarch64 1.47.1-3.fc41 fedora 239.3 KiB
libcurl aarch64 8.10.1-1.fc42 fedora 858.4 KiB
libeconf aarch64 0.6.2-3.fc41 fedora 206.1 KiB
libevent aarch64 2.1.12-14.fc41 fedora 1.5 MiB
libfdisk aarch64 2.40.2-8.fc42 fedora 482.9 KiB
libffi aarch64 3.4.6-3.fc42 fedora 282.4 KiB
libgcc aarch64 14.2.1-3.fc42 fedora 350.2 KiB
libgomp aarch64 14.2.1-3.fc42 fedora 567.3 KiB
libidn2 aarch64 2.3.7-2.fc41 fedora 457.2 KiB
libmount aarch64 2.40.2-8.fc42 fedora 483.9 KiB
libnghttp2 aarch64 1.63.0-1.fc42 fedora 262.2 KiB
libnsl2 aarch64 2.0.1-2.fc41 fedora 222.0 KiB
libpkgconf aarch64 2.3.0-1.fc42 fedora 198.1 KiB
libpsl aarch64 0.21.5-4.fc41 fedora 196.6 KiB
libpwquality aarch64 1.4.5-11.fc41 fedora 1.1 MiB
libselinux aarch64 3.7-6.fc42 fedora 265.1 KiB
libsemanage aarch64 3.7-3.fc42 fedora 361.6 KiB
libsepol aarch64 3.7-3.fc42 fedora 873.9 KiB
libsmartcols aarch64 2.40.2-8.fc42 fedora 288.5 KiB
libssh aarch64 0.11.1-1.fc42 fedora 649.6 KiB
libssh-config noarch 0.11.1-1.fc42 fedora 277.0 B
libstdc++ aarch64 14.2.1-3.fc42 fedora 2.8 MiB
libtasn1 aarch64 4.19.0-9.fc41 fedora 283.8 KiB
libtirpc aarch64 1.3.5-0.fc41 fedora 274.8 KiB
libtool-ltdl aarch64 2.4.7-12.fc41 fedora 222.2 KiB
libunistring aarch64 1.1-8.fc41 fedora 1.8 MiB
libuuid aarch64 2.40.2-8.fc42 fedora 197.5 KiB
libverto aarch64 0.3.2-9.fc41 fedora 197.5 KiB
libxcrypt aarch64 4.4.36-7.fc41 fedora 399.0 KiB
libxml2 aarch64 2.12.8-2.fc41 fedora 2.1 MiB
libzstd aarch64 1.5.6-2.fc41 fedora 796.0 KiB
lua-libs aarch64 5.4.6-6.fc41 fedora 393.1 KiB
lua-srpm-macros noarch 1-14.fc41 fedora 1.3 KiB
lz4-libs aarch64 1.10.0-1.fc41 fedora 261.6 KiB
mpfr aarch64 4.2.1-5.fc41 fedora 818.9 KiB
ncurses-base noarch 6.5-2.20240629.fc41 fedora 326.3 KiB
ncurses-libs aarch64 6.5-2.20240629.fc41 fedora 2.2 MiB
ocaml-srpm-macros noarch 10-3.fc41 fedora 1.9 KiB
openblas-srpm-macros noarch 2-18.fc41 fedora 112.0 B
openldap aarch64 2.6.8-5.fc41 fedora 952.3 KiB
openssl-libs aarch64 1:3.2.2-8.fc42 fedora 7.2 MiB
p11-kit aarch64 0.25.5-3.fc41 fedora 2.6 MiB
p11-kit-trust aarch64 0.25.5-3.fc41 fedora 655.6 KiB
package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB
pam aarch64 1.6.1-6.fc42 fedora 11.0 MiB
pam-libs aarch64 1.6.1-6.fc42 fedora 607.3 KiB
pcre2 aarch64 10.44-1.fc41.1 fedora 905.5 KiB
pcre2-syntax noarch 10.44-1.fc41.1 fedora 251.6 KiB
perl-srpm-macros noarch 1-56.fc41 fedora 861.0 B
pkgconf aarch64 2.3.0-1.fc42 fedora 240.6 KiB
pkgconf-m4 noarch 2.3.0-1.fc42 fedora 14.4 KiB
pkgconf-pkg-config aarch64 2.3.0-1.fc42 fedora 990.0 B
popt aarch64 1.19-7.fc41 fedora 272.9 KiB
publicsuffix-list-dafsa noarch 20240107-4.fc41 fedora 67.5 KiB
pyproject-srpm-macros noarch 1.15.0-1.fc42 fedora 1.9 KiB
python-srpm-macros noarch 3.13-3.fc41 fedora 51.0 KiB
qt5-srpm-macros noarch 5.15.15-1.fc42 fedora 500.0 B
qt6-srpm-macros noarch 6.7.2-3.fc41 fedora 456.0 B
readline aarch64 8.2-11.fc42 fedora 753.3 KiB
rpm aarch64 4.19.94-1.fc42 fedora 3.9 MiB
rpm-build-libs aarch64 4.19.94-1.fc42 fedora 262.7 KiB
rpm-libs aarch64 4.19.94-1.fc42 fedora 798.0 KiB
rpm-sequoia aarch64 1.7.0-2.fc41 fedora 2.3 MiB
rust-srpm-macros noarch 26.3-3.fc42 fedora 4.8 KiB
setup noarch 2.15.0-5.fc41 fedora 720.7 KiB
sqlite-libs aarch64 3.46.0-4.fc41 fedora 1.6 MiB
systemd-libs aarch64 256.5-1.fc42 fedora 2.5 MiB
util-linux-core aarch64 2.40.2-8.fc42 fedora 6.2 MiB
xxhash-libs aarch64 0.8.2-3.fc41 fedora 212.3 KiB
xz-libs aarch64 1:5.6.2-2.fc41 fedora 266.4 KiB
zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB
zip aarch64 3.0-41.fc41 fedora 1.1 MiB
zlib-ng-compat aarch64 2.2.2-1.fc42 copr_base 197.6 KiB
zstd aarch64 1.5.6-2.fc41 fedora 1.7 MiB
Installing groups:
Buildsystem building group
Transaction Summary:
Installing: 153 packages
Total size of inbound packages is 53 MiB. Need to download 53 MiB.
After this operation, 303 MiB extra will be used (install 303 MiB, remove 0 B).
[ 1/153] bzip2-0:1.0.8-19.fc41.aarch64 100% | 2.8 MiB/s | 52.4 KiB | 00m00s
[ 2/153] bash-0:5.2.32-2.fc42.aarch64 100% | 74.6 MiB/s | 1.8 MiB | 00m00s
[ 3/153] cpio-0:2.15-2.fc41.aarch64 100% | 47.4 MiB/s | 291.3 KiB | 00m00s
[ 4/153] coreutils-0:9.5-9.fc42.aarch6 100% | 42.7 MiB/s | 1.2 MiB | 00m00s
[ 5/153] fedora-release-common-0:42-0. 100% | 11.2 MiB/s | 23.0 KiB | 00m00s
[ 6/153] diffutils-0:3.10-8.fc41.aarch 100% | 98.4 MiB/s | 402.9 KiB | 00m00s
[ 7/153] findutils-1:4.10.0-4.fc41.aar 100% | 135.3 MiB/s | 554.1 KiB | 00m00s
[ 8/153] gawk-0:5.3.0-4.fc41.aarch64 100% | 132.2 MiB/s | 1.1 MiB | 00m00s
[ 9/153] glibc-minimal-langpack-0:2.40 100% | 16.9 MiB/s | 120.9 KiB | 00m00s
[ 10/153] grep-0:3.11-9.fc41.aarch64 100% | 58.2 MiB/s | 297.9 KiB | 00m00s
[ 11/153] gzip-0:1.13-2.fc41.aarch64 100% | 33.0 MiB/s | 169.1 KiB | 00m00s
[ 12/153] info-0:7.1.1-1.fc42.aarch64 100% | 35.4 MiB/s | 181.2 KiB | 00m00s
[ 13/153] patch-0:2.7.6-25.fc41.aarch64 100% | 25.2 MiB/s | 128.8 KiB | 00m00s
[ 14/153] redhat-rpm-config-0:295-1.fc4 100% | 20.1 MiB/s | 82.4 KiB | 00m00s
[ 15/153] rpm-build-0:4.19.94-1.fc42.aa 100% | 20.6 MiB/s | 84.4 KiB | 00m00s
[ 16/153] sed-0:4.9-3.fc41.aarch64 100% | 51.3 MiB/s | 315.4 KiB | 00m00s
[ 17/153] shadow-utils-2:4.16.0-4.fc42. 100% | 131.8 MiB/s | 1.3 MiB | 00m00s
[ 18/153] tar-2:1.35-4.fc41.aarch64 100% | 69.6 MiB/s | 854.7 KiB | 00m00s
[ 19/153] unzip-0:6.0-64.fc41.aarch64 100% | 20.1 MiB/s | 184.8 KiB | 00m00s
[ 20/153] util-linux-0:2.40.2-8.fc42.aa 100% | 167.5 MiB/s | 1.2 MiB | 00m00s
[ 21/153] which-0:2.21-42.fc41.aarch64 100% | 8.1 MiB/s | 41.5 KiB | 00m00s
[ 22/153] xz-1:5.6.2-2.fc41.aarch64 100% | 76.9 MiB/s | 472.8 KiB | 00m00s
[ 23/153] filesystem-0:3.18-29.fc42.aar 100% | 155.3 MiB/s | 1.1 MiB | 00m00s
[ 24/153] glibc-0:2.40.9000-1.fc42.aarc 100% | 157.1 MiB/s | 1.9 MiB | 00m00s
[ 25/153] ncurses-libs-0:6.5-2.20240629 100% | 29.0 MiB/s | 326.5 KiB | 00m00s
[ 26/153] bzip2-libs-0:1.0.8-19.fc41.aa 100% | 6.9 MiB/s | 42.7 KiB | 00m00s
[ 27/153] coreutils-common-0:9.5-9.fc42 100% | 235.7 MiB/s | 2.1 MiB | 00m00s
[ 28/153] gmp-1:6.3.0-2.fc41.aarch64 100% | 33.0 MiB/s | 270.1 KiB | 00m00s
[ 29/153] libacl-0:2.3.2-2.fc41.aarch64 100% | 3.0 MiB/s | 24.9 KiB | 00m00s
[ 30/153] libattr-0:2.5.2-4.fc41.aarch6 100% | 17.8 MiB/s | 18.2 KiB | 00m00s
[ 31/153] libcap-0:2.70-4.fc41.aarch64 100% | 28.4 MiB/s | 87.2 KiB | 00m00s
[ 32/153] libselinux-0:3.7-6.fc42.aarch 100% | 28.6 MiB/s | 87.9 KiB | 00m00s
[ 33/153] openssl-libs-1:3.2.2-8.fc42.a 100% | 243.0 MiB/s | 2.2 MiB | 00m00s
[ 34/153] fedora-repos-0:42-0.2.noarch 100% | 1.3 MiB/s | 9.2 KiB | 00m00s
[ 35/153] systemd-libs-0:256.5-1.fc42.a 100% | 69.4 MiB/s | 710.4 KiB | 00m00s
[ 36/153] mpfr-0:4.2.1-5.fc41.aarch64 100% | 105.7 MiB/s | 324.8 KiB | 00m00s
[ 37/153] readline-0:8.2-11.fc42.aarch6 100% | 69.3 MiB/s | 212.7 KiB | 00m00s
[ 38/153] glibc-common-0:2.40.9000-1.fc 100% | 97.3 MiB/s | 398.7 KiB | 00m00s
[ 39/153] pcre2-0:10.44-1.fc41.1.aarch6 100% | 73.9 MiB/s | 227.0 KiB | 00m00s
[ 40/153] ansible-srpm-macros-0:1-16.fc 100% | 20.3 MiB/s | 20.8 KiB | 00m00s
[ 41/153] ed-0:1.20.2-2.fc41.aarch64 100% | 19.8 MiB/s | 81.2 KiB | 00m00s
[ 42/153] build-reproducibility-srpm-ma 100% | 10.4 MiB/s | 10.6 KiB | 00m00s
[ 43/153] dwz-0:0.15-7.fc41.aarch64 100% | 66.5 MiB/s | 136.3 KiB | 00m00s
[ 44/153] efi-srpm-macros-0:5-12.fc41.n 100% | 10.9 MiB/s | 22.4 KiB | 00m00s
[ 45/153] file-0:5.45-7.fc41.aarch64 100% | 24.1 MiB/s | 49.5 KiB | 00m00s
[ 46/153] fonts-srpm-macros-1:2.0.5-17. 100% | 26.3 MiB/s | 27.0 KiB | 00m00s
[ 47/153] forge-srpm-macros-0:0.3.2-1.f 100% | 19.2 MiB/s | 19.7 KiB | 00m00s
[ 48/153] fpc-srpm-macros-0:1.3-13.fc41 100% | 7.8 MiB/s | 8.0 KiB | 00m00s
[ 49/153] ghc-srpm-macros-0:1.9.2-1.fc4 100% | 8.9 MiB/s | 9.1 KiB | 00m00s
[ 50/153] gnat-srpm-macros-0:6-6.fc41.n 100% | 8.7 MiB/s | 9.0 KiB | 00m00s
[ 51/153] go-srpm-macros-0:3.6.0-3.fc41 100% | 27.3 MiB/s | 28.0 KiB | 00m00s
[ 52/153] kernel-srpm-macros-0:1.0-24.f 100% | 9.6 MiB/s | 9.9 KiB | 00m00s
[ 53/153] lua-srpm-macros-0:1-14.fc41.n 100% | 8.7 MiB/s | 8.9 KiB | 00m00s
[ 54/153] ocaml-srpm-macros-0:10-3.fc41 100% | 9.0 MiB/s | 9.2 KiB | 00m00s
[ 55/153] openblas-srpm-macros-0:2-18.f 100% | 7.5 MiB/s | 7.7 KiB | 00m00s
[ 56/153] package-notes-srpm-macros-0:0 100% | 9.6 MiB/s | 9.8 KiB | 00m00s
[ 57/153] perl-srpm-macros-0:1-56.fc41. 100% | 8.3 MiB/s | 8.5 KiB | 00m00s
[ 58/153] pyproject-srpm-macros-0:1.15. 100% | 13.2 MiB/s | 13.5 KiB | 00m00s
[ 59/153] python-srpm-macros-0:3.13-3.f 100% | 23.2 MiB/s | 23.7 KiB | 00m00s
[ 60/153] qt5-srpm-macros-0:5.15.15-1.f 100% | 4.3 MiB/s | 8.9 KiB | 00m00s
[ 61/153] qt6-srpm-macros-0:6.7.2-3.fc4 100% | 3.0 MiB/s | 9.1 KiB | 00m00s
[ 62/153] rust-srpm-macros-0:26.3-3.fc4 100% | 5.9 MiB/s | 12.1 KiB | 00m00s
[ 63/153] zig-srpm-macros-0:1-3.fc41.no 100% | 7.9 MiB/s | 8.1 KiB | 00m00s
[ 64/153] rpm-0:4.19.94-1.fc42.aarch64 100% | 107.3 MiB/s | 549.4 KiB | 00m00s
[ 65/153] zip-0:3.0-41.fc41.aarch64 100% | 51.5 MiB/s | 263.7 KiB | 00m00s
[ 66/153] debugedit-0:5.0-17.fc41.aarch 100% | 15.5 MiB/s | 79.4 KiB | 00m00s
[ 67/153] elfutils-0:0.191-8.fc41.aarch 100% | 87.3 MiB/s | 536.1 KiB | 00m00s
[ 68/153] elfutils-libelf-0:0.191-8.fc4 100% | 50.7 MiB/s | 207.7 KiB | 00m00s
[ 69/153] libarchive-0:3.7.6-1.fc42.aar 100% | 99.7 MiB/s | 408.3 KiB | 00m00s
[ 70/153] pkgconf-pkg-config-0:2.3.0-1. 100% | 1.9 MiB/s | 10.0 KiB | 00m00s
[ 71/153] popt-0:1.19-7.fc41.aarch64 100% | 8.1 MiB/s | 66.0 KiB | 00m00s
[ 72/153] rpm-build-libs-0:4.19.94-1.fc 100% | 11.7 MiB/s | 95.5 KiB | 00m00s
[ 73/153] rpm-libs-0:4.19.94-1.fc42.aar 100% | 59.2 MiB/s | 303.0 KiB | 00m00s
[ 74/153] libeconf-0:0.6.2-3.fc41.aarch 100% | 31.6 MiB/s | 32.3 KiB | 00m00s
[ 75/153] zstd-0:1.5.6-2.fc41.aarch64 100% | 111.5 MiB/s | 456.8 KiB | 00m00s
[ 76/153] audit-libs-0:4.0.2-1.fc41.aar 100% | 30.9 MiB/s | 126.6 KiB | 00m00s
[ 77/153] libsemanage-0:3.7-3.fc42.aarc 100% | 55.8 MiB/s | 114.3 KiB | 00m00s
[ 78/153] pam-libs-0:1.6.1-6.fc42.aarch 100% | 56.0 MiB/s | 57.3 KiB | 00m00s
[ 79/153] libxcrypt-0:4.4.36-7.fc41.aar 100% | 60.1 MiB/s | 123.1 KiB | 00m00s
[ 80/153] setup-0:2.15.0-5.fc41.noarch 100% | 75.4 MiB/s | 154.4 KiB | 00m00s
[ 81/153] authselect-libs-0:1.5.0-7.fc4 100% | 71.0 MiB/s | 218.1 KiB | 00m00s
[ 82/153] libcap-ng-0:0.8.5-3.fc41.aarc 100% | 16.0 MiB/s | 32.8 KiB | 00m00s
[ 83/153] libblkid-0:2.40.2-8.fc42.aarc 100% | 40.4 MiB/s | 124.3 KiB | 00m00s
[ 84/153] libfdisk-0:2.40.2-8.fc42.aarc 100% | 76.0 MiB/s | 155.7 KiB | 00m00s
[ 85/153] libmount-0:2.40.2-8.fc42.aarc 100% | 75.5 MiB/s | 154.6 KiB | 00m00s
[ 86/153] libsmartcols-0:2.40.2-8.fc42. 100% | 27.0 MiB/s | 82.9 KiB | 00m00s
[ 87/153] libuuid-0:2.40.2-8.fc42.aarch 100% | 28.8 MiB/s | 29.5 KiB | 00m00s
[ 88/153] pam-0:1.6.1-6.fc42.aarch64 100% | 137.9 MiB/s | 564.8 KiB | 00m00s
[ 89/153] util-linux-core-0:2.40.2-8.fc 100% | 129.9 MiB/s | 532.1 KiB | 00m00s
[ 90/153] xz-libs-1:5.6.2-2.fc41.aarch6 100% | 21.7 MiB/s | 111.0 KiB | 00m00s
[ 91/153] basesystem-0:11-21.fc41.noarc 100% | 1.4 MiB/s | 7.4 KiB | 00m00s
[ 92/153] glibc-gconv-extra-0:2.40.9000 100% | 227.6 MiB/s | 2.0 MiB | 00m00s
[ 93/153] libgcc-0:14.2.1-3.fc42.aarch6 100% | 14.2 MiB/s | 116.2 KiB | 00m00s
[ 94/153] ncurses-base-0:6.5-2.20240629 100% | 21.6 MiB/s | 88.4 KiB | 00m00s
[ 95/153] libsepol-0:3.7-3.fc42.aarch64 100% | 106.4 MiB/s | 326.8 KiB | 00m00s
[ 96/153] ca-certificates-0:2024.2.69_v 100% | 153.7 MiB/s | 944.3 KiB | 00m00s
[ 97/153] crypto-policies-0:20240828-1. 100% | 15.4 MiB/s | 94.6 KiB | 00m00s
[ 98/153] fedora-gpg-keys-0:42-0.2.noar 100% | 26.1 MiB/s | 133.6 KiB | 00m00s
[ 99/153] fedora-repos-rawhide-0:42-0.2 100% | 8.5 MiB/s | 8.7 KiB | 00m00s
[100/153] pcre2-syntax-0:10.44-1.fc41.1 100% | 48.8 MiB/s | 149.9 KiB | 00m00s
[101/153] add-determinism-0:0.3.6-1.fc4 100% | 154.6 MiB/s | 791.3 KiB | 00m00s
[102/153] file-libs-0:5.45-7.fc41.aarch 100% | 124.0 MiB/s | 761.6 KiB | 00m00s
[103/153] curl-0:8.10.1-1.fc42.aarch64 100% | 35.4 MiB/s | 217.8 KiB | 00m00s
[104/153] elfutils-libs-0:0.191-8.fc41. 100% | 63.0 MiB/s | 258.1 KiB | 00m00s
[105/153] elfutils-debuginfod-client-0: 100% | 18.0 MiB/s | 36.9 KiB | 00m00s
[106/153] libstdc++-0:14.2.1-3.fc42.aar 100% | 162.6 MiB/s | 832.3 KiB | 00m00s
[107/153] libzstd-0:1.5.6-2.fc41.aarch6 100% | 70.3 MiB/s | 288.0 KiB | 00m00s
[108/153] libxml2-0:2.12.8-2.fc41.aarch 100% | 94.6 MiB/s | 677.8 KiB | 00m00s
[109/153] lz4-libs-0:1.10.0-1.fc41.aarc 100% | 23.5 MiB/s | 72.3 KiB | 00m00s
[110/153] pkgconf-0:2.3.0-1.fc42.aarch6 100% | 14.7 MiB/s | 45.2 KiB | 00m00s
[111/153] pkgconf-m4-0:2.3.0-1.fc42.noa 100% | 4.7 MiB/s | 14.3 KiB | 00m00s
[112/153] libgomp-0:14.2.1-3.fc42.aarch 100% | 67.2 MiB/s | 344.2 KiB | 00m00s
[113/153] lua-libs-0:5.4.6-6.fc41.aarch 100% | 21.1 MiB/s | 129.8 KiB | 00m00s
[114/153] rpm-sequoia-0:1.7.0-2.fc41.aa 100% | 166.7 MiB/s | 853.7 KiB | 00m00s
[115/153] sqlite-libs-0:3.46.0-4.fc41.a 100% | 137.8 MiB/s | 705.6 KiB | 00m00s
[116/153] authselect-0:1.5.0-7.fc41.aar 100% | 28.5 MiB/s | 145.8 KiB | 00m00s
[117/153] gdbm-1:1.23-7.fc41.aarch64 100% | 49.3 MiB/s | 151.6 KiB | 00m00s
[118/153] gdbm-libs-1:1.23-7.fc41.aarch 100% | 54.9 MiB/s | 56.3 KiB | 00m00s
[119/153] libnsl2-0:2.0.1-2.fc41.aarch6 100% | 14.7 MiB/s | 30.1 KiB | 00m00s
[120/153] libffi-0:3.4.6-3.fc42.aarch64 100% | 18.7 MiB/s | 38.3 KiB | 00m00s
[121/153] libpwquality-0:1.4.5-11.fc41. 100% | 29.2 MiB/s | 119.8 KiB | 00m00s
[122/153] libtirpc-0:1.3.5-0.fc41.aarch 100% | 18.7 MiB/s | 95.7 KiB | 00m00s
[123/153] p11-kit-0:0.25.5-3.fc41.aarch 100% | 155.9 MiB/s | 478.8 KiB | 00m00s
[124/153] p11-kit-trust-0:0.25.5-3.fc41 100% | 43.5 MiB/s | 133.8 KiB | 00m00s
[125/153] elfutils-default-yama-scope-0 100% | 6.0 MiB/s | 12.3 KiB | 00m00s
[126/153] libpkgconf-0:2.3.0-1.fc42.aar 100% | 37.5 MiB/s | 38.4 KiB | 00m00s
[127/153] cracklib-0:2.9.11-6.fc41.aarc 100% | 30.1 MiB/s | 92.6 KiB | 00m00s
[128/153] libcom_err-0:1.47.1-3.fc41.aa 100% | 13.0 MiB/s | 26.7 KiB | 00m00s
[129/153] krb5-libs-0:1.21.3-2.fc41.aar 100% | 148.9 MiB/s | 762.4 KiB | 00m00s
[130/153] alternatives-0:1.30-1.fc41.aa 100% | 20.3 MiB/s | 41.5 KiB | 00m00s
[131/153] libtasn1-0:4.19.0-9.fc41.aarc 100% | 23.8 MiB/s | 73.0 KiB | 00m00s
[132/153] keyutils-libs-0:1.6.3-4.fc41. 100% | 31.1 MiB/s | 31.9 KiB | 00m00s
[133/153] libverto-0:0.3.2-9.fc41.aarch 100% | 20.5 MiB/s | 20.9 KiB | 00m00s
[134/153] jansson-0:2.13.1-10.fc41.aarc 100% | 22.4 MiB/s | 45.9 KiB | 00m00s
[135/153] fedora-release-0:42-0.3.noarc 100% | 11.9 MiB/s | 12.2 KiB | 00m00s
[136/153] zlib-ng-compat-0:2.2.2-1.fc42 100% | 7.2 MiB/s | 66.3 KiB | 00m00s
[137/153] gdb-minimal-0:15.1-2.fc42.aar 100% | 218.1 MiB/s | 4.1 MiB | 00m00s
[138/153] xxhash-libs-0:0.8.2-3.fc41.aa 100% | 2.1 MiB/s | 34.6 KiB | 00m00s
[139/153] fedora-release-identity-basic 100% | 6.4 MiB/s | 13.0 KiB | 00m00s
[140/153] libcurl-0:8.10.1-1.fc42.aarch 100% | 70.8 MiB/s | 362.6 KiB | 00m00s
[141/153] libbrotli-0:1.1.0-5.fc41.aarc 100% | 84.5 MiB/s | 346.2 KiB | 00m00s
[142/153] libidn2-0:2.3.7-2.fc41.aarch6 100% | 58.0 MiB/s | 118.8 KiB | 00m00s
[143/153] libnghttp2-0:1.63.0-1.fc42.aa 100% | 25.0 MiB/s | 76.7 KiB | 00m00s
[144/153] libpsl-0:0.21.5-4.fc41.aarch6 100% | 31.5 MiB/s | 64.4 KiB | 00m00s
[145/153] libssh-0:0.11.1-1.fc42.aarch6 100% | 75.9 MiB/s | 233.0 KiB | 00m00s
[146/153] openldap-0:2.6.8-5.fc41.aarch 100% | 82.0 MiB/s | 251.8 KiB | 00m00s
[147/153] publicsuffix-list-dafsa-0:202 100% | 56.9 MiB/s | 58.3 KiB | 00m00s
[148/153] libunistring-0:1.1-8.fc41.aar 100% | 131.8 MiB/s | 539.8 KiB | 00m00s
[149/153] libssh-config-0:0.11.1-1.fc42 100% | 9.2 MiB/s | 9.4 KiB | 00m00s
[150/153] binutils-0:2.43.50-1.fc42.aar 100% | 125.8 MiB/s | 6.8 MiB | 00m00s
[151/153] cyrus-sasl-lib-0:2.1.28-27.fc 100% | 69.3 MiB/s | 780.2 KiB | 00m00s
[152/153] libevent-0:2.1.12-14.fc41.aar 100% | 20.7 MiB/s | 254.6 KiB | 00m00s
[153/153] libtool-ltdl-0:2.4.7-12.fc41. 100% | 11.7 MiB/s | 35.8 KiB | 00m00s
--------------------------------------------------------------------------------
[153/153] Total 100% | 153.1 MiB/s | 52.8 MiB | 00m00s
Running transaction
Importing PGP key 0x105EF944:
UserID : "Fedora (42) <fedora-42-primary@fedoraproject.org>"
Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944
From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary
The key was successfully imported.
Importing PGP key 0x105EF944:
UserID : "Fedora (42) <fedora-42-primary@fedoraproject.org>"
Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944
From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary
The key was successfully imported.
Importing PGP key 0xE99D6AD1:
UserID : "Fedora (41) <fedora-41-primary@fedoraproject.org>"
Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1
From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary
The key was successfully imported.
Importing PGP key 0x31645531:
UserID : "Fedora (43) <fedora-43-primary@fedoraproject.org>"
Fingerprint: C6E7F081CF80E13146676E88829B606631645531
From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary
The key was successfully imported.
[ 1/155] Verify package files 100% | 692.0 B/s | 153.0 B | 00m00s
[ 2/155] Prepare transaction 100% | 2.4 KiB/s | 153.0 B | 00m00s
[ 3/155] Installing libgcc-0:14.2.1-3. 100% | 171.8 MiB/s | 351.9 KiB | 00m00s
[ 4/155] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s
[ 5/155] Installing publicsuffix-list- 100% | 66.7 MiB/s | 68.3 KiB | 00m00s
[ 6/155] Installing fedora-release-ide 100% | 0.0 B/s | 952.0 B | 00m00s
[ 7/155] Installing fedora-repos-rawhi 100% | 2.4 MiB/s | 2.4 KiB | 00m00s
[ 8/155] Installing fedora-gpg-keys-0: 100% | 28.0 MiB/s | 172.2 KiB | 00m00s
[ 9/155] Installing fedora-repos-0:42- 100% | 0.0 B/s | 5.7 KiB | 00m00s
[ 10/155] Installing fedora-release-com 100% | 23.1 MiB/s | 23.7 KiB | 00m00s
[ 11/155] Installing fedora-release-0:4 100% | 0.0 B/s | 124.0 B | 00m00s
[ 12/155] Installing setup-0:2.15.0-5.f 100% | 44.3 MiB/s | 726.1 KiB | 00m00s
[ 13/155] Installing filesystem-0:3.18- 100% | 2.2 MiB/s | 212.6 KiB | 00m00s
[ 14/155] Installing basesystem-0:11-21 100% | 0.0 B/s | 124.0 B | 00m00s
[ 15/155] Installing pkgconf-m4-0:2.3.0 100% | 0.0 B/s | 14.8 KiB | 00m00s
[ 16/155] Installing pcre2-syntax-0:10. 100% | 124.1 MiB/s | 254.1 KiB | 00m00s
[ 17/155] Installing ncurses-base-0:6.5 100% | 49.1 MiB/s | 351.7 KiB | 00m00s
[ 18/155] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s
[ 19/155] Installing ncurses-libs-0:6.5 100% | 281.1 MiB/s | 2.2 MiB | 00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
[ 20/155] Installing glibc-0:2.40.9000- 100% | 250.4 MiB/s | 9.3 MiB | 00m00s
[ 21/155] Installing bash-0:5.2.32-2.fc 100% | 296.9 MiB/s | 8.3 MiB | 00m00s
[ 22/155] Installing glibc-common-0:2.4 100% | 285.6 MiB/s | 2.6 MiB | 00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
[ 23/155] Installing glibc-gconv-extra- 100% | 535.4 MiB/s | 49.3 MiB | 00m00s
[ 24/155] Installing zlib-ng-compat-0:2 100% | 193.8 MiB/s | 198.5 KiB | 00m00s
[ 25/155] Installing bzip2-libs-0:1.0.8 100% | 197.1 MiB/s | 201.9 KiB | 00m00s
[ 26/155] Installing xz-libs-1:5.6.2-2. 100% | 261.2 MiB/s | 267.5 KiB | 00m00s
[ 27/155] Installing readline-0:8.2-11. 100% | 245.9 MiB/s | 755.5 KiB | 00m00s
[ 28/155] Installing popt-0:1.19-7.fc41 100% | 68.2 MiB/s | 279.5 KiB | 00m00s
[ 29/155] Installing libuuid-0:2.40.2-8 100% | 194.0 MiB/s | 198.6 KiB | 00m00s
[ 30/155] Installing libblkid-0:2.40.2- 100% | 204.9 MiB/s | 419.7 KiB | 00m00s
[ 31/155] Installing gmp-1:6.3.0-2.fc41 100% | 235.8 MiB/s | 724.2 KiB | 00m00s
[ 32/155] Installing libattr-0:2.5.2-4. 100% | 192.9 MiB/s | 197.5 KiB | 00m00s
[ 33/155] Installing libacl-0:2.3.2-2.f 100% | 192.3 MiB/s | 196.9 KiB | 00m00s
[ 34/155] Installing libxcrypt-0:4.4.36 100% | 196.1 MiB/s | 401.7 KiB | 00m00s
[ 35/155] Installing libstdc++-0:14.2.1 100% | 277.4 MiB/s | 2.8 MiB | 00m00s
[ 36/155] Installing libzstd-0:1.5.6-2. 100% | 259.5 MiB/s | 797.3 KiB | 00m00s
[ 37/155] Installing elfutils-libelf-0: 100% | 328.5 MiB/s | 1.3 MiB | 00m00s
[ 38/155] Installing libeconf-0:0.6.2-3 100% | 202.9 MiB/s | 207.8 KiB | 00m00s
[ 39/155] Installing gdbm-libs-1:1.23-7 100% | 417.7 MiB/s | 427.7 KiB | 00m00s
[ 40/155] Installing dwz-0:0.15-7.fc41. 100% | 189.5 MiB/s | 388.1 KiB | 00m00s
[ 41/155] Installing mpfr-0:4.2.1-5.fc4 100% | 267.1 MiB/s | 820.5 KiB | 00m00s
[ 42/155] Installing gawk-0:5.3.0-4.fc4 100% | 355.3 MiB/s | 4.3 MiB | 00m00s
[ 43/155] Installing unzip-0:6.0-64.fc4 100% | 237.7 MiB/s | 730.2 KiB | 00m00s
[ 44/155] Installing file-libs-0:5.45-7 100% | 527.6 MiB/s | 10.0 MiB | 00m00s
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[ 46/155] Installing crypto-policies-0: 100% | 19.9 MiB/s | 163.2 KiB | 00m00s
[ 47/155] Installing pcre2-0:10.44-1.fc 100% | 295.2 MiB/s | 906.9 KiB | 00m00s
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[ 50/155] Installing libcap-ng-0:0.8.5- 100% | 204.6 MiB/s | 419.1 KiB | 00m00s
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[ 52/155] Installing pam-libs-0:1.6.1-6 100% | 297.6 MiB/s | 609.5 KiB | 00m00s
[ 53/155] Installing libcap-0:2.70-4.fc 100% | 344.0 MiB/s | 1.4 MiB | 00m00s
[ 54/155] Installing systemd-libs-0:256 100% | 280.1 MiB/s | 2.5 MiB | 00m00s
[ 55/155] Installing libsmartcols-0:2.4 100% | 282.9 MiB/s | 289.7 KiB | 00m00s
[ 56/155] Installing libsepol-0:3.7-3.f 100% | 284.8 MiB/s | 874.9 KiB | 00m00s
[ 57/155] Installing libselinux-0:3.7-6 100% | 130.0 MiB/s | 266.3 KiB | 00m00s
[ 58/155] Installing sed-0:4.9-3.fc41.a 100% | 164.3 MiB/s | 1.0 MiB | 00m00s
[ 59/155] Installing findutils-1:4.10.0 100% | 234.2 MiB/s | 2.1 MiB | 00m00s
[ 60/155] Installing libmount-0:2.40.2- 100% | 236.8 MiB/s | 485.1 KiB | 00m00s
[ 61/155] Installing lz4-libs-0:1.10.0- 100% | 256.5 MiB/s | 262.7 KiB | 00m00s
[ 62/155] Installing lua-libs-0:5.4.6-6 100% | 192.5 MiB/s | 394.3 KiB | 00m00s
[ 63/155] Installing libffi-0:3.4.6-3.f 100% | 277.2 MiB/s | 283.8 KiB | 00m00s
[ 64/155] Installing libcom_err-0:1.47. 100% | 234.8 MiB/s | 240.4 KiB | 00m00s
[ 65/155] Installing libtasn1-0:4.19.0- 100% | 139.4 MiB/s | 285.6 KiB | 00m00s
[ 66/155] Installing p11-kit-0:0.25.5-3 100% | 220.5 MiB/s | 2.6 MiB | 00m00s
[ 67/155] Installing alternatives-0:1.3 100% | 214.7 MiB/s | 219.9 KiB | 00m00s
[ 68/155] Installing libunistring-0:1.1 100% | 301.5 MiB/s | 1.8 MiB | 00m00s
[ 69/155] Installing libidn2-0:2.3.7-2. 100% | 113.1 MiB/s | 463.1 KiB | 00m00s
[ 70/155] Installing libpsl-0:0.21.5-4. 100% | 193.1 MiB/s | 197.7 KiB | 00m00s
[ 71/155] Installing p11-kit-trust-0:0. 100% | 64.2 MiB/s | 657.4 KiB | 00m00s
[ 72/155] Installing zstd-0:1.5.6-2.fc4 100% | 241.6 MiB/s | 1.7 MiB | 00m00s
[ 73/155] Installing util-linux-core-0: 100% | 387.7 MiB/s | 6.2 MiB | 00m00s
[ 74/155] Installing tar-2:1.35-4.fc41. 100% | 255.6 MiB/s | 3.1 MiB | 00m00s
[ 75/155] Installing libsemanage-0:3.7- 100% | 118.3 MiB/s | 363.3 KiB | 00m00s
[ 76/155] Installing shadow-utils-2:4.1 100% | 244.9 MiB/s | 7.3 MiB | 00m00s
[ 77/155] Installing zip-0:3.0-41.fc41. 100% | 281.0 MiB/s | 1.1 MiB | 00m00s
[ 78/155] Installing gdbm-1:1.23-7.fc41 100% | 182.3 MiB/s | 933.4 KiB | 00m00s
[ 79/155] Installing cyrus-sasl-lib-0:2 100% | 310.7 MiB/s | 3.1 MiB | 00m00s
[ 80/155] Installing libfdisk-0:2.40.2- 100% | 236.3 MiB/s | 483.9 KiB | 00m00s
[ 81/155] Installing libxml2-0:2.12.8-2 100% | 267.7 MiB/s | 2.1 MiB | 00m00s
[ 82/155] Installing bzip2-0:1.0.8-19.f 100% | 211.0 MiB/s | 432.2 KiB | 00m00s
[ 83/155] Installing add-determinism-0: 100% | 290.5 MiB/s | 2.0 MiB | 00m00s
[ 84/155] Installing build-reproducibil 100% | 0.0 B/s | 1.0 KiB | 00m00s
[ 85/155] Installing sqlite-libs-0:3.46 100% | 259.8 MiB/s | 1.6 MiB | 00m00s
[ 86/155] Installing ed-0:1.20.2-2.fc41 100% | 139.2 MiB/s | 285.1 KiB | 00m00s
[ 87/155] Installing patch-0:2.7.6-25.f 100% | 191.5 MiB/s | 392.1 KiB | 00m00s
[ 88/155] Installing elfutils-default-y 100% | 291.9 KiB/s | 2.0 KiB | 00m00s
[ 89/155] Installing elfutils-libs-0:0. 100% | 229.5 MiB/s | 940.2 KiB | 00m00s
[ 90/155] Installing cpio-0:2.15-2.fc41 100% | 174.4 MiB/s | 1.2 MiB | 00m00s
[ 91/155] Installing diffutils-0:3.10-8 100% | 234.4 MiB/s | 2.1 MiB | 00m00s
[ 92/155] Installing libgomp-0:14.2.1-3 100% | 277.7 MiB/s | 568.7 KiB | 00m00s
[ 93/155] Installing libpkgconf-0:2.3.0 100% | 194.6 MiB/s | 199.2 KiB | 00m00s
[ 94/155] Installing pkgconf-0:2.3.0-1. 100% | 118.7 MiB/s | 243.1 KiB | 00m00s
[ 95/155] Installing pkgconf-pkg-config 100% | 1.7 MiB/s | 1.8 KiB | 00m00s
[ 96/155] Installing keyutils-libs-0:1. 100% | 222.5 MiB/s | 227.9 KiB | 00m00s
[ 97/155] Installing libverto-0:0.3.2-9 100% | 194.7 MiB/s | 199.3 KiB | 00m00s
[ 98/155] Installing jansson-0:2.13.1-1 100% | 216.7 MiB/s | 221.9 KiB | 00m00s
[ 99/155] Installing xxhash-libs-0:0.8. 100% | 208.7 MiB/s | 213.7 KiB | 00m00s
[100/155] Installing libbrotli-0:1.1.0- 100% | 285.2 MiB/s | 1.1 MiB | 00m00s
[101/155] Installing libnghttp2-0:1.63. 100% | 257.2 MiB/s | 263.3 KiB | 00m00s
[102/155] Installing libtool-ltdl-0:2.4 100% | 218.1 MiB/s | 223.4 KiB | 00m00s
[103/155] Installing rust-srpm-macros-0 100% | 0.0 B/s | 5.6 KiB | 00m00s
[104/155] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 732.0 B | 00m00s
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[106/155] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s
[107/155] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s
[108/155] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s
[109/155] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s
[110/155] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s
[111/155] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s
[112/155] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s
[113/155] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s
[114/155] Installing ansible-srpm-macro 100% | 35.4 MiB/s | 36.2 KiB | 00m00s
[115/155] Installing coreutils-common-0 100% | 286.9 MiB/s | 11.2 MiB | 00m00s
[116/155] Installing openssl-libs-1:3.2 100% | 313.5 MiB/s | 7.2 MiB | 00m00s
[117/155] Installing coreutils-0:9.5-9. 100% | 442.6 MiB/s | 20.8 MiB | 00m00s
[118/155] Installing ca-certificates-0: 100% | 1.3 MiB/s | 2.4 MiB | 00m02s
[119/155] Installing krb5-libs-0:1.21.3 100% | 257.4 MiB/s | 3.3 MiB | 00m00s
[120/155] Installing libarchive-0:3.7.6 100% | 238.5 MiB/s | 976.8 KiB | 00m00s
[121/155] Installing libtirpc-0:1.3.5-0 100% | 135.0 MiB/s | 276.5 KiB | 00m00s
[122/155] Installing gzip-0:1.13-2.fc41 100% | 120.7 MiB/s | 494.4 KiB | 00m00s
[123/155] Installing authselect-libs-0: 100% | 115.6 MiB/s | 946.8 KiB | 00m00s
[124/155] Installing cracklib-0:2.9.11- 100% | 132.0 MiB/s | 946.3 KiB | 00m00s
[125/155] Installing libpwquality-0:1.4 100% | 158.2 MiB/s | 1.1 MiB | 00m00s
[126/155] Installing libnsl2-0:2.0.1-2. 100% | 109.0 MiB/s | 223.2 KiB | 00m00s
[127/155] Installing pam-0:1.6.1-6.fc42 100% | 344.9 MiB/s | 11.0 MiB | 00m00s
[128/155] Installing libssh-0:0.11.1-1. 100% | 212.1 MiB/s | 651.7 KiB | 00m00s
[129/155] Installing rpm-sequoia-0:1.7. 100% | 287.1 MiB/s | 2.3 MiB | 00m00s
[130/155] Installing rpm-libs-0:4.19.94 100% | 260.3 MiB/s | 799.5 KiB | 00m00s
[131/155] Installing rpm-build-libs-0:4 100% | 128.7 MiB/s | 263.6 KiB | 00m00s
[132/155] Installing libevent-0:2.1.12- 100% | 304.7 MiB/s | 1.5 MiB | 00m00s
[133/155] Installing openldap-0:2.6.8-5 100% | 233.4 MiB/s | 956.1 KiB | 00m00s
[134/155] Installing libcurl-0:8.10.1-1 100% | 279.8 MiB/s | 859.5 KiB | 00m00s
[135/155] Installing elfutils-debuginfo 100% | 194.8 MiB/s | 398.9 KiB | 00m00s
[136/155] Installing elfutils-0:0.191-8 100% | 412.9 MiB/s | 5.0 MiB | 00m00s
[137/155] Installing binutils-0:2.43.50 100% | 334.1 MiB/s | 32.7 MiB | 00m00s
[138/155] Installing gdb-minimal-0:15.1 100% | 301.8 MiB/s | 13.0 MiB | 00m00s
[139/155] Installing debugedit-0:5.0-17 100% | 245.1 MiB/s | 502.0 KiB | 00m00s
[140/155] Installing curl-0:8.10.1-1.fc 100% | 43.9 MiB/s | 583.8 KiB | 00m00s
[141/155] Installing rpm-0:4.19.94-1.fc 100% | 139.9 MiB/s | 3.4 MiB | 00m00s
[142/155] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.2 KiB | 00m00s
[143/155] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s
[144/155] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s
[145/155] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s
[146/155] Installing forge-srpm-macros- 100% | 39.4 MiB/s | 40.4 KiB | 00m00s
[147/155] Installing go-srpm-macros-0:3 100% | 60.5 MiB/s | 62.0 KiB | 00m00s
[148/155] Installing python-srpm-macros 100% | 50.9 MiB/s | 52.2 KiB | 00m00s
[149/155] Installing redhat-rpm-config- 100% | 62.9 MiB/s | 193.2 KiB | 00m00s
[150/155] Installing rpm-build-0:4.19.9 100% | 279.4 MiB/s | 1.4 MiB | 00m00s
[151/155] Installing pyproject-srpm-mac 100% | 1.2 MiB/s | 2.5 KiB | 00m00s
[152/155] Installing util-linux-0:2.40. 100% | 346.0 MiB/s | 17.0 MiB | 00m00s
[153/155] Installing authselect-0:1.5.0 100% | 102.2 MiB/s | 313.9 KiB | 00m00s
[154/155] Installing which-0:2.21-42.fc 100% | 122.2 MiB/s | 250.4 KiB | 00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
[155/155] Installing info-0:7.1.1-1.fc4 100% | 264.1 KiB/s | 614.1 KiB | 00m02s
Warning: skipped PGP checks for 2 packages from repository: copr_base
Complete!
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: add-determinism-0.3.6-1.fc41.aarch64
alternatives-1.30-1.fc41.aarch64
ansible-srpm-macros-1-16.fc41.noarch
audit-libs-4.0.2-1.fc41.aarch64
authselect-1.5.0-7.fc41.aarch64
authselect-libs-1.5.0-7.fc41.aarch64
basesystem-11-21.fc41.noarch
bash-5.2.32-2.fc42.aarch64
binutils-2.43.50-1.fc42.aarch64
build-reproducibility-srpm-macros-0.3.6-1.fc41.noarch
bzip2-1.0.8-19.fc41.aarch64
bzip2-libs-1.0.8-19.fc41.aarch64
ca-certificates-2024.2.69_v8.0.401-1.fc42.noarch
coreutils-9.5-9.fc42.aarch64
coreutils-common-9.5-9.fc42.aarch64
cpio-2.15-2.fc41.aarch64
cracklib-2.9.11-6.fc41.aarch64
crypto-policies-20240828-1.git5f66e81.fc42.noarch
curl-8.10.1-1.fc42.aarch64
cyrus-sasl-lib-2.1.28-27.fc41.aarch64
debugedit-5.0-17.fc41.aarch64
diffutils-3.10-8.fc41.aarch64
dwz-0.15-7.fc41.aarch64
ed-1.20.2-2.fc41.aarch64
efi-srpm-macros-5-12.fc41.noarch
elfutils-0.191-8.fc41.aarch64
elfutils-debuginfod-client-0.191-8.fc41.aarch64
elfutils-default-yama-scope-0.191-8.fc41.noarch
elfutils-libelf-0.191-8.fc41.aarch64
elfutils-libs-0.191-8.fc41.aarch64
fedora-gpg-keys-42-0.2.noarch
fedora-release-42-0.3.noarch
fedora-release-common-42-0.3.noarch
fedora-release-identity-basic-42-0.3.noarch
fedora-repos-42-0.2.noarch
fedora-repos-rawhide-42-0.2.noarch
file-5.45-7.fc41.aarch64
file-libs-5.45-7.fc41.aarch64
filesystem-3.18-29.fc42.aarch64
findutils-4.10.0-4.fc41.aarch64
fonts-srpm-macros-2.0.5-17.fc41.noarch
forge-srpm-macros-0.3.2-1.fc41.noarch
fpc-srpm-macros-1.3-13.fc41.noarch
gawk-5.3.0-4.fc41.aarch64
gdb-minimal-15.1-2.fc42.aarch64
gdbm-1.23-7.fc41.aarch64
gdbm-libs-1.23-7.fc41.aarch64
ghc-srpm-macros-1.9.2-1.fc42.noarch
glibc-2.40.9000-1.fc42.aarch64
glibc-common-2.40.9000-1.fc42.aarch64
glibc-gconv-extra-2.40.9000-1.fc42.aarch64
glibc-minimal-langpack-2.40.9000-1.fc42.aarch64
gmp-6.3.0-2.fc41.aarch64
gnat-srpm-macros-6-6.fc41.noarch
go-srpm-macros-3.6.0-3.fc41.noarch
gpg-pubkey-105ef944-65ca83d1
gpg-pubkey-31645531-66b6dccf
gpg-pubkey-e99d6ad1-64d2612c
grep-3.11-9.fc41.aarch64
gzip-1.13-2.fc41.aarch64
info-7.1.1-1.fc42.aarch64
jansson-2.13.1-10.fc41.aarch64
kernel-srpm-macros-1.0-24.fc41.noarch
keyutils-libs-1.6.3-4.fc41.aarch64
krb5-libs-1.21.3-2.fc41.aarch64
libacl-2.3.2-2.fc41.aarch64
libarchive-3.7.6-1.fc42.aarch64
libattr-2.5.2-4.fc41.aarch64
libblkid-2.40.2-8.fc42.aarch64
libbrotli-1.1.0-5.fc41.aarch64
libcap-2.70-4.fc41.aarch64
libcap-ng-0.8.5-3.fc41.aarch64
libcom_err-1.47.1-3.fc41.aarch64
libcurl-8.10.1-1.fc42.aarch64
libeconf-0.6.2-3.fc41.aarch64
libevent-2.1.12-14.fc41.aarch64
libfdisk-2.40.2-8.fc42.aarch64
libffi-3.4.6-3.fc42.aarch64
libgcc-14.2.1-3.fc42.aarch64
libgomp-14.2.1-3.fc42.aarch64
libidn2-2.3.7-2.fc41.aarch64
libmount-2.40.2-8.fc42.aarch64
libnghttp2-1.63.0-1.fc42.aarch64
libnsl2-2.0.1-2.fc41.aarch64
libpkgconf-2.3.0-1.fc42.aarch64
libpsl-0.21.5-4.fc41.aarch64
libpwquality-1.4.5-11.fc41.aarch64
libselinux-3.7-6.fc42.aarch64
libsemanage-3.7-3.fc42.aarch64
libsepol-3.7-3.fc42.aarch64
libsmartcols-2.40.2-8.fc42.aarch64
libssh-0.11.1-1.fc42.aarch64
libssh-config-0.11.1-1.fc42.noarch
libstdc++-14.2.1-3.fc42.aarch64
libtasn1-4.19.0-9.fc41.aarch64
libtirpc-1.3.5-0.fc41.aarch64
libtool-ltdl-2.4.7-12.fc41.aarch64
libunistring-1.1-8.fc41.aarch64
libuuid-2.40.2-8.fc42.aarch64
libverto-0.3.2-9.fc41.aarch64
libxcrypt-4.4.36-7.fc41.aarch64
libxml2-2.12.8-2.fc41.aarch64
libzstd-1.5.6-2.fc41.aarch64
lua-libs-5.4.6-6.fc41.aarch64
lua-srpm-macros-1-14.fc41.noarch
lz4-libs-1.10.0-1.fc41.aarch64
mpfr-4.2.1-5.fc41.aarch64
ncurses-base-6.5-2.20240629.fc41.noarch
ncurses-libs-6.5-2.20240629.fc41.aarch64
ocaml-srpm-macros-10-3.fc41.noarch
openblas-srpm-macros-2-18.fc41.noarch
openldap-2.6.8-5.fc41.aarch64
openssl-libs-3.2.2-8.fc42.aarch64
p11-kit-0.25.5-3.fc41.aarch64
p11-kit-trust-0.25.5-3.fc41.aarch64
package-notes-srpm-macros-0.5-12.fc41.noarch
pam-1.6.1-6.fc42.aarch64
pam-libs-1.6.1-6.fc42.aarch64
patch-2.7.6-25.fc41.aarch64
pcre2-10.44-1.fc41.1.aarch64
pcre2-syntax-10.44-1.fc41.1.noarch
perl-srpm-macros-1-56.fc41.noarch
pkgconf-2.3.0-1.fc42.aarch64
pkgconf-m4-2.3.0-1.fc42.noarch
pkgconf-pkg-config-2.3.0-1.fc42.aarch64
popt-1.19-7.fc41.aarch64
publicsuffix-list-dafsa-20240107-4.fc41.noarch
pyproject-srpm-macros-1.15.0-1.fc42.noarch
python-srpm-macros-3.13-3.fc41.noarch
qt5-srpm-macros-5.15.15-1.fc42.noarch
qt6-srpm-macros-6.7.2-3.fc41.noarch
readline-8.2-11.fc42.aarch64
redhat-rpm-config-295-1.fc42.noarch
rpm-4.19.94-1.fc42.aarch64
rpm-build-4.19.94-1.fc42.aarch64
rpm-build-libs-4.19.94-1.fc42.aarch64
rpm-libs-4.19.94-1.fc42.aarch64
rpm-sequoia-1.7.0-2.fc41.aarch64
rust-srpm-macros-26.3-3.fc42.noarch
sed-4.9-3.fc41.aarch64
setup-2.15.0-5.fc41.noarch
shadow-utils-4.16.0-4.fc42.aarch64
sqlite-libs-3.46.0-4.fc41.aarch64
systemd-libs-256.5-1.fc42.aarch64
tar-1.35-4.fc41.aarch64
unzip-6.0-64.fc41.aarch64
util-linux-2.40.2-8.fc42.aarch64
util-linux-core-2.40.2-8.fc42.aarch64
which-2.21-42.fc41.aarch64
xxhash-libs-0.8.2-3.fc41.aarch64
xz-5.6.2-2.fc41.aarch64
xz-libs-5.6.2-2.fc41.aarch64
zig-srpm-macros-1-3.fc41.noarch
zip-3.0-41.fc41.aarch64
zlib-ng-compat-2.2.2-1.fc42.aarch64
zstd-1.5.6-2.fc41.aarch64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1721174400
Wrote: /builddir/build/SRPMS/bcftools-1.15.1-10.fc42.src.rpm
Finish: rpmbuild -bs
cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-rawhide-aarch64-1727274377.320064/root/var/log’: No such file or directory
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-aarch64-1727274377.320064/root/var/log/dnf5.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-441cyqx1/bcftools/bcftools.spec) Config(child) 0 minutes 22 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-1.15.1-10.fc42.src.rpm) Config(fedora-rawhide-aarch64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1727274377.320064/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1727274377.320064/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-1727274377.320064/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 downloaded with a bootstrap image:
rpm-4.19.94-1.fc42.aarch64
rpm-sequoia-1.7.0-2.fc41.aarch64
dnf5-5.2.6.2-1.fc42.aarch64
dnf5-plugins-5.2.6.2-1.fc42.aarch64
Finish: chroot init
Start: build phase for bcftools-1.15.1-10.fc42.src.rpm
Start: build setup for bcftools-1.15.1-10.fc42.src.rpm
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1721174400
Wrote: /builddir/build/SRPMS/bcftools-1.15.1-10.fc42.src.rpm
Updating and loading repositories:
fedora 100% | 236.9 KiB/s | 10.9 KiB | 00m00s
Copr repository 100% | 109.4 KiB/s | 1.5 KiB | 00m00s
Repositories loaded.
Package Arch Version Repository Size
Installing:
gcc aarch64 14.2.1-3.fc42 fedora 93.8 MiB
gsl-devel aarch64 2.7.1-11.fc41 fedora 1.6 MiB
htslib-devel aarch64 1.15.1-6.fc41 fedora 411.0 KiB
htslib-tools aarch64 1.15.1-6.fc41 fedora 2.5 MiB
make aarch64 1:4.4.1-8.fc41 fedora 1.8 MiB
perl-ExtUtils-Embed noarch 1.35-511.fc41 fedora 15.5 KiB
perl-File-Temp noarch 1:0.231.100-511.fc41 fedora 162.3 KiB
perl-FindBin noarch 1.54-511.fc41 fedora 6.7 KiB
perl-Getopt-Long noarch 1:2.58-2.fc41 fedora 144.5 KiB
perl-interpreter aarch64 4:5.40.0-511.fc41 fedora 302.3 KiB
zlib-ng-compat-devel aarch64 2.2.2-1.fc42 copr_base 106.8 KiB
Installing dependencies:
annobin-docs noarch 12.70-1.fc42 fedora 97.7 KiB
annobin-plugin-gcc aarch64 12.70-1.fc42 fedora 1.1 MiB
autoconf noarch 2.72-3.fc41 fedora 2.8 MiB
automake noarch 1.16.5-17.fc41 fedora 1.7 MiB
cmake-filesystem aarch64 3.28.3-7.fc41 fedora 0.0 B
cpp aarch64 14.2.1-3.fc42 fedora 31.8 MiB
emacs-filesystem noarch 1:30.0-3.fc41 fedora 0.0 B
expat aarch64 2.6.3-1.fc42 fedora 539.6 KiB
gcc-plugin-annobin aarch64 14.2.1-3.fc42 fedora 197.1 KiB
glibc-devel aarch64 2.40.9000-1.fc42 fedora 2.2 MiB
groff-base aarch64 1.23.0-7.fc41 fedora 5.2 MiB
gsl aarch64 2.7.1-11.fc41 fedora 3.7 MiB
htslib aarch64 1.15.1-6.fc41 fedora 1.8 MiB
kernel-headers aarch64 6.11.0-63.fc42 fedora 6.3 MiB
libasan aarch64 14.2.1-3.fc42 fedora 1.6 MiB
libatomic aarch64 14.2.1-3.fc42 fedora 196.9 KiB
libb2 aarch64 0.98.1-12.fc41 fedora 202.2 KiB
libmpc aarch64 1.3.1-6.fc41 fedora 280.8 KiB
libubsan aarch64 14.2.1-3.fc42 fedora 539.3 KiB
libxcrypt-devel aarch64 4.4.36-7.fc41 fedora 30.3 KiB
m4 aarch64 1.4.19-10.fc41 fedora 668.7 KiB
mpdecimal aarch64 2.5.1-16.fc41 fedora 328.9 KiB
ncurses aarch64 6.5-2.20240629.fc41 fedora 1.7 MiB
perl-AutoLoader noarch 5.74-511.fc41 fedora 20.5 KiB
perl-AutoSplit noarch 5.74-511.fc41 fedora 23.1 KiB
perl-B aarch64 1.89-511.fc41 fedora 606.1 KiB
perl-Benchmark noarch 1.25-511.fc41 fedora 36.3 KiB
perl-Carp noarch 1.54-511.fc41 fedora 46.6 KiB
perl-Class-Struct noarch 0.68-511.fc41 fedora 25.4 KiB
perl-Data-Dumper aarch64 2.189-512.fc41 fedora 263.8 KiB
perl-Devel-PPPort aarch64 3.72-512.fc41 fedora 980.3 KiB
perl-Digest noarch 1.20-511.fc41 fedora 35.3 KiB
perl-Digest-MD5 aarch64 2.59-5.fc41 fedora 231.9 KiB
perl-DynaLoader aarch64 1.56-511.fc41 fedora 32.1 KiB
perl-Encode aarch64 4:3.21-511.fc41 fedora 5.9 MiB
perl-Errno aarch64 1.38-511.fc41 fedora 8.4 KiB
perl-Exporter noarch 5.78-511.fc41 fedora 54.3 KiB
perl-ExtUtils-Command noarch 2:7.70-512.fc41 fedora 9.6 KiB
perl-ExtUtils-Constant noarch 0.25-511.fc41 fedora 85.8 KiB
perl-ExtUtils-Install noarch 2.22-511.fc41 fedora 85.5 KiB
perl-ExtUtils-MakeMaker noarch 2:7.70-512.fc41 fedora 734.1 KiB
perl-ExtUtils-Manifest noarch 1:1.75-511.fc41 fedora 84.8 KiB
perl-ExtUtils-ParseXS noarch 1:3.51-511.fc41 fedora 399.7 KiB
perl-Fcntl aarch64 1.18-511.fc41 fedora 221.1 KiB
perl-File-Basename noarch 2.86-511.fc41 fedora 14.0 KiB
perl-File-Compare noarch 1.100.800-511.fc41 fedora 5.6 KiB
perl-File-Copy noarch 2.41-511.fc41 fedora 19.6 KiB
perl-File-Find noarch 1.44-511.fc41 fedora 41.9 KiB
perl-File-Path noarch 2.18-511.fc41 fedora 63.5 KiB
perl-File-stat noarch 1.14-511.fc41 fedora 12.5 KiB
perl-FileHandle noarch 2.05-511.fc41 fedora 9.3 KiB
perl-Getopt-Std noarch 1.14-511.fc41 fedora 11.2 KiB
perl-HTTP-Tiny noarch 0.088-512.fc41 fedora 152.2 KiB
perl-IO aarch64 1.55-511.fc41 fedora 319.2 KiB
perl-IO-Socket-IP noarch 0.42-512.fc41 fedora 98.7 KiB
perl-IO-Socket-SSL noarch 2.089-1.fc42 fedora 703.3 KiB
perl-IPC-Open3 noarch 1.22-511.fc41 fedora 22.5 KiB
perl-MIME-Base32 noarch 1.303-21.fc41 fedora 30.7 KiB
perl-MIME-Base64 aarch64 3.16-511.fc41 fedora 222.2 KiB
perl-Mozilla-CA noarch 20240730-1.fc41 fedora 9.8 KiB
perl-Net-SSLeay aarch64 1.94-7.fc41 fedora 1.4 MiB
perl-POSIX aarch64 2.20-511.fc41 fedora 327.3 KiB
perl-PathTools aarch64 3.91-511.fc41 fedora 352.1 KiB
perl-Pod-Escapes noarch 1:1.07-511.fc41 fedora 24.9 KiB
perl-Pod-Perldoc noarch 3.28.01-512.fc41 fedora 163.7 KiB
perl-Pod-Simple noarch 1:3.45-511.fc41 fedora 560.9 KiB
perl-Pod-Usage noarch 4:2.03-511.fc41 fedora 84.8 KiB
perl-Scalar-List-Utils aarch64 5:1.66-1.fc42 fedora 278.7 KiB
perl-SelectSaver noarch 1.02-511.fc41 fedora 2.2 KiB
perl-Socket aarch64 4:2.038-511.fc41 fedora 272.1 KiB
perl-Storable aarch64 1:3.32-511.fc41 fedora 372.5 KiB
perl-Symbol noarch 1.09-511.fc41 fedora 6.8 KiB
perl-Term-ANSIColor noarch 5.01-512.fc41 fedora 97.5 KiB
perl-Term-Cap noarch 1.18-511.fc41 fedora 29.3 KiB
perl-Test-Harness noarch 1:3.50-1.fc42 fedora 559.6 KiB
perl-Text-ParseWords noarch 3.31-511.fc41 fedora 13.6 KiB
perl-Text-Tabs+Wrap noarch 2024.001-511.fc41 fedora 22.6 KiB
perl-Thread-Queue noarch 3.14-511.fc41 fedora 28.9 KiB
perl-Time-Local noarch 2:1.350-511.fc41 fedora 69.0 KiB
perl-URI noarch 5.29-1.fc42 fedora 251.9 KiB
perl-base noarch 2.27-511.fc41 fedora 12.5 KiB
perl-constant noarch 1.33-512.fc41 fedora 26.2 KiB
perl-devel aarch64 4:5.40.0-511.fc41 fedora 8.0 MiB
perl-if noarch 0.61.000-511.fc41 fedora 5.8 KiB
perl-lib aarch64 0.65-511.fc41 fedora 8.5 KiB
perl-libnet noarch 3.15-512.fc41 fedora 289.4 KiB
perl-libs aarch64 4:5.40.0-511.fc41 fedora 10.9 MiB
perl-locale noarch 1.12-511.fc41 fedora 6.5 KiB
perl-mro aarch64 1.29-511.fc41 fedora 209.7 KiB
perl-overload noarch 1.37-511.fc41 fedora 71.5 KiB
perl-overloading noarch 0.02-511.fc41 fedora 4.8 KiB
perl-parent noarch 1:0.242-1.fc42 fedora 10.0 KiB
perl-podlators noarch 1:6.0.2-2.fc41 fedora 317.5 KiB
perl-threads aarch64 1:2.40-511.fc41 fedora 263.2 KiB
perl-threads-shared aarch64 1.69-511.fc41 fedora 231.8 KiB
perl-vars noarch 1.05-511.fc41 fedora 3.9 KiB
perl-version aarch64 9:0.99.33-1.fc42 fedora 288.9 KiB
python-pip-wheel noarch 24.2-2.fc42 fedora 1.2 MiB
python3 aarch64 3.13.0~rc2-3.fc42 fedora 211.8 KiB
python3-libs aarch64 3.13.0~rc2-3.fc42 fedora 49.8 MiB
python3-pyparsing noarch 3.1.2-7.fc41 fedora 1.0 MiB
systemtap-sdt-devel aarch64 5.2~pre17250223gd07e4284-1.fc42 fedora 182.4 KiB
systemtap-sdt-dtrace aarch64 5.2~pre17250223gd07e4284-1.fc42 fedora 178.9 KiB
tzdata noarch 2024a-9.fc41 fedora 1.7 MiB
Transaction Summary:
Installing: 115 packages
Total size of inbound packages is 75 MiB. Need to download 75 MiB.
After this operation, 255 MiB extra will be used (install 255 MiB, remove 0 B).
[ 1/115] htslib-devel-0:1.15.1-6.fc41. 100% | 4.8 MiB/s | 104.2 KiB | 00m00s
[ 2/115] gsl-devel-0:2.7.1-11.fc41.aar 100% | 26.6 MiB/s | 653.0 KiB | 00m00s
[ 3/115] htslib-tools-0:1.15.1-6.fc41. 100% | 44.7 MiB/s | 549.4 KiB | 00m00s
[ 4/115] make-1:4.4.1-8.fc41.aarch64 100% | 47.5 MiB/s | 583.7 KiB | 00m00s
[ 5/115] perl-ExtUtils-Embed-0:1.35-51 100% | 3.4 MiB/s | 17.6 KiB | 00m00s
[ 6/115] perl-File-Temp-1:0.231.100-51 100% | 9.6 MiB/s | 59.1 KiB | 00m00s
[ 7/115] perl-FindBin-0:1.54-511.fc41. 100% | 2.8 MiB/s | 14.2 KiB | 00m00s
[ 8/115] perl-Getopt-Long-1:2.58-2.fc4 100% | 12.5 MiB/s | 63.9 KiB | 00m00s
[ 9/115] perl-interpreter-4:5.40.0-511 100% | 10.1 MiB/s | 72.4 KiB | 00m00s
[ 10/115] zlib-ng-compat-devel-0:2.2.2- 100% | 4.7 MiB/s | 38.6 KiB | 00m00s
[ 11/115] glibc-devel-0:2.40.9000-1.fc4 100% | 38.9 MiB/s | 637.1 KiB | 00m00s
[ 12/115] libasan-0:14.2.1-3.fc42.aarch 100% | 13.5 MiB/s | 495.9 KiB | 00m00s
[ 13/115] cpp-0:14.2.1-3.fc42.aarch64 100% | 157.5 MiB/s | 10.7 MiB | 00m00s
[ 14/115] libatomic-0:14.2.1-3.fc42.aar 100% | 1.9 MiB/s | 43.9 KiB | 00m00s
[ 15/115] libmpc-0:1.3.1-6.fc41.aarch64 100% | 3.9 MiB/s | 72.7 KiB | 00m00s
[ 16/115] gcc-0:14.2.1-3.fc42.aarch64 100% | 196.3 MiB/s | 33.8 MiB | 00m00s
[ 17/115] libubsan-0:14.2.1-3.fc42.aarc 100% | 5.6 MiB/s | 217.8 KiB | 00m00s
[ 18/115] automake-0:1.16.5-17.fc41.noa 100% | 19.4 MiB/s | 696.9 KiB | 00m00s
[ 19/115] gsl-0:2.7.1-11.fc41.aarch64 100% | 146.5 MiB/s | 1.0 MiB | 00m00s
[ 20/115] perl-Exporter-0:5.78-511.fc41 100% | 10.1 MiB/s | 30.9 KiB | 00m00s
[ 21/115] perl-PathTools-0:3.91-511.fc4 100% | 28.5 MiB/s | 87.5 KiB | 00m00s
[ 22/115] htslib-0:1.15.1-6.fc41.aarch6 100% | 33.8 MiB/s | 484.4 KiB | 00m00s
[ 23/115] perl-Carp-0:1.54-511.fc41.noa 100% | 9.4 MiB/s | 28.9 KiB | 00m00s
[ 24/115] perl-Errno-0:1.38-511.fc41.aa 100% | 7.3 MiB/s | 14.9 KiB | 00m00s
[ 25/115] perl-libs-4:5.40.0-511.fc41.a 100% | 176.1 MiB/s | 2.3 MiB | 00m00s
[ 26/115] perl-Fcntl-0:1.18-511.fc41.aa 100% | 9.8 MiB/s | 30.0 KiB | 00m00s
[ 27/115] perl-devel-4:5.40.0-511.fc41. 100% | 39.3 MiB/s | 764.2 KiB | 00m00s
[ 28/115] perl-File-Path-0:2.18-511.fc4 100% | 11.5 MiB/s | 35.3 KiB | 00m00s
[ 29/115] perl-IO-0:1.55-511.fc41.aarch 100% | 20.0 MiB/s | 82.0 KiB | 00m00s
[ 30/115] perl-POSIX-0:2.20-511.fc41.aa 100% | 31.6 MiB/s | 97.0 KiB | 00m00s
[ 31/115] perl-constant-0:1.33-512.fc41 100% | 7.5 MiB/s | 23.0 KiB | 00m00s
[ 32/115] perl-overload-0:1.37-511.fc41 100% | 14.8 MiB/s | 45.5 KiB | 00m00s
[ 33/115] perl-Scalar-List-Utils-5:1.66 100% | 11.6 MiB/s | 71.3 KiB | 00m00s
[ 34/115] perl-parent-1:0.242-1.fc42.no 100% | 3.7 MiB/s | 15.0 KiB | 00m00s
[ 35/115] perl-File-Basename-0:2.86-511 100% | 5.6 MiB/s | 17.1 KiB | 00m00s
[ 36/115] perl-Pod-Usage-4:2.03-511.fc4 100% | 7.8 MiB/s | 40.0 KiB | 00m00s
[ 37/115] perl-Text-ParseWords-0:3.31-5 100% | 5.4 MiB/s | 16.6 KiB | 00m00s
[ 38/115] perl-base-0:2.27-511.fc41.noa 100% | 7.9 MiB/s | 16.2 KiB | 00m00s
[ 39/115] cmake-filesystem-0:3.28.3-7.f 100% | 17.8 MiB/s | 18.2 KiB | 00m00s
[ 40/115] libxcrypt-devel-0:4.4.36-7.fc 100% | 9.4 MiB/s | 28.8 KiB | 00m00s
[ 41/115] autoconf-0:2.72-3.fc41.noarch 100% | 115.8 MiB/s | 829.7 KiB | 00m00s
[ 42/115] kernel-headers-0:6.11.0-63.fc 100% | 144.8 MiB/s | 1.6 MiB | 00m00s
[ 43/115] perl-Class-Struct-0:0.68-511. 100% | 2.7 MiB/s | 22.0 KiB | 00m00s
[ 44/115] perl-File-stat-0:1.14-511.fc4 100% | 5.5 MiB/s | 17.0 KiB | 00m00s
[ 45/115] perl-Thread-Queue-0:3.14-511. 100% | 6.9 MiB/s | 21.3 KiB | 00m00s
[ 46/115] perl-threads-1:2.40-511.fc41. 100% | 18.7 MiB/s | 57.4 KiB | 00m00s
[ 47/115] perl-ExtUtils-Constant-0:0.25 100% | 21.3 MiB/s | 43.7 KiB | 00m00s
[ 48/115] perl-ExtUtils-ParseXS-1:3.51- 100% | 45.7 MiB/s | 187.3 KiB | 00m00s
[ 49/115] perl-File-Compare-0:1.100.800 100% | 12.9 MiB/s | 13.2 KiB | 00m00s
[ 50/115] perl-Text-Tabs+Wrap-0:2024.00 100% | 21.3 MiB/s | 21.9 KiB | 00m00s
[ 51/115] perl-vars-0:1.05-511.fc41.noa 100% | 6.3 MiB/s | 13.0 KiB | 00m00s
[ 52/115] perl-Devel-PPPort-0:3.72-512. 100% | 11.8 MiB/s | 216.7 KiB | 00m00s
[ 53/115] perl-ExtUtils-Install-0:2.22- 100% | 2.8 MiB/s | 43.6 KiB | 00m00s
[ 54/115] systemtap-sdt-devel-0:5.2~pre 100% | 16.4 MiB/s | 67.3 KiB | 00m00s
[ 55/115] perl-DynaLoader-0:1.56-511.fc 100% | 8.5 MiB/s | 26.0 KiB | 00m00s
[ 56/115] perl-Encode-4:3.21-511.fc41.a 100% | 130.1 MiB/s | 1.0 MiB | 00m00s
[ 57/115] perl-SelectSaver-0:1.02-511.f 100% | 1.6 MiB/s | 11.7 KiB | 00m00s
[ 58/115] perl-Symbol-0:1.09-511.fc41.n 100% | 13.8 MiB/s | 14.2 KiB | 00m00s
[ 59/115] perl-Socket-4:2.038-511.fc41. 100% | 13.5 MiB/s | 55.5 KiB | 00m00s
[ 60/115] perl-locale-0:1.12-511.fc41.n 100% | 6.6 MiB/s | 13.6 KiB | 00m00s
[ 61/115] systemtap-sdt-dtrace-0:5.2~pr 100% | 4.1 MiB/s | 68.0 KiB | 00m00s
[ 62/115] perl-mro-0:1.29-511.fc41.aarc 100% | 28.9 MiB/s | 29.6 KiB | 00m00s
[ 63/115] perl-Pod-Perldoc-0:3.28.01-51 100% | 42.0 MiB/s | 86.1 KiB | 00m00s
[ 64/115] perl-overloading-0:0.02-511.f 100% | 4.2 MiB/s | 12.9 KiB | 00m00s
[ 65/115] perl-podlators-1:6.0.2-2.fc41 100% | 41.9 MiB/s | 128.8 KiB | 00m00s
[ 66/115] emacs-filesystem-1:30.0-3.fc4 100% | 2.3 MiB/s | 7.1 KiB | 00m00s
[ 67/115] perl-Data-Dumper-0:2.189-512. 100% | 53.8 MiB/s | 55.1 KiB | 00m00s
[ 68/115] m4-0:1.4.19-10.fc41.aarch64 100% | 58.9 MiB/s | 301.4 KiB | 00m00s
[ 69/115] perl-File-Find-0:1.44-511.fc4 100% | 12.3 MiB/s | 25.3 KiB | 00m00s
[ 70/115] perl-threads-shared-0:1.69-51 100% | 21.7 MiB/s | 44.3 KiB | 00m00s
[ 71/115] perl-File-Copy-0:2.41-511.fc4 100% | 2.8 MiB/s | 20.1 KiB | 00m00s
[ 72/115] perl-ExtUtils-MakeMaker-2:7.7 100% | 71.5 MiB/s | 292.9 KiB | 00m00s
[ 73/115] python3-0:3.13.0~rc2-3.fc42.a 100% | 13.6 MiB/s | 27.9 KiB | 00m00s
[ 74/115] perl-Getopt-Std-0:1.14-511.fc 100% | 5.1 MiB/s | 15.6 KiB | 00m00s
[ 75/115] python3-pyparsing-0:3.1.2-7.f 100% | 45.1 MiB/s | 277.4 KiB | 00m00s
[ 76/115] perl-MIME-Base64-0:3.16-511.f 100% | 9.8 MiB/s | 30.2 KiB | 00m00s
[ 77/115] perl-AutoSplit-0:5.74-511.fc4 100% | 1.5 MiB/s | 21.6 KiB | 00m00s
[ 78/115] perl-Storable-1:3.32-511.fc41 100% | 31.7 MiB/s | 97.4 KiB | 00m00s
[ 79/115] perl-HTTP-Tiny-0:0.088-512.fc 100% | 27.3 MiB/s | 55.8 KiB | 00m00s
[ 80/115] groff-base-0:1.23.0-7.fc41.aa 100% | 153.6 MiB/s | 1.1 MiB | 00m00s
[ 81/115] perl-IPC-Open3-0:1.22-511.fc4 100% | 4.3 MiB/s | 21.8 KiB | 00m00s
[ 82/115] perl-Pod-Simple-1:3.45-511.fc 100% | 42.8 MiB/s | 219.0 KiB | 00m00s
[ 83/115] perl-Term-Cap-0:1.18-511.fc41 100% | 21.6 MiB/s | 22.1 KiB | 00m00s
[ 84/115] perl-Term-ANSIColor-0:5.01-51 100% | 23.3 MiB/s | 47.7 KiB | 00m00s
[ 85/115] perl-B-0:1.89-511.fc41.aarch6 100% | 57.7 MiB/s | 177.2 KiB | 00m00s
[ 86/115] perl-ExtUtils-Command-2:7.70- 100% | 4.6 MiB/s | 14.1 KiB | 00m00s
[ 87/115] perl-Test-Harness-1:3.50-1.fc 100% | 67.6 MiB/s | 277.0 KiB | 00m00s
[ 88/115] perl-lib-0:0.65-511.fc41.aarc 100% | 7.3 MiB/s | 14.9 KiB | 00m00s
[ 89/115] perl-version-9:0.99.33-1.fc42 100% | 30.5 MiB/s | 62.5 KiB | 00m00s
[ 90/115] perl-IO-Socket-SSL-0:2.089-1. 100% | 56.4 MiB/s | 231.2 KiB | 00m00s
[ 91/115] perl-ExtUtils-Manifest-1:1.75 100% | 2.1 MiB/s | 34.1 KiB | 00m00s
[ 92/115] perl-Mozilla-CA-0:20240730-1. 100% | 4.6 MiB/s | 14.3 KiB | 00m00s
[ 93/115] perl-Net-SSLeay-0:1.94-7.fc41 100% | 45.8 MiB/s | 375.4 KiB | 00m00s
[ 94/115] perl-Time-Local-2:1.350-511.f 100% | 3.7 MiB/s | 34.5 KiB | 00m00s
[ 95/115] perl-if-0:0.61.000-511.fc41.n 100% | 1.9 MiB/s | 14.0 KiB | 00m00s
[ 96/115] perl-Pod-Escapes-1:1.07-511.f 100% | 2.1 MiB/s | 19.8 KiB | 00m00s
[ 97/115] perl-Benchmark-0:1.25-511.fc4 100% | 6.5 MiB/s | 26.7 KiB | 00m00s
[ 98/115] ncurses-0:6.5-2.20240629.fc41 100% | 59.0 MiB/s | 422.6 KiB | 00m00s
[ 99/115] python3-libs-0:3.13.0~rc2-3.f 100% | 195.5 MiB/s | 9.0 MiB | 00m00s
[100/115] libb2-0:0.98.1-12.fc41.aarch6 100% | 2.7 MiB/s | 24.9 KiB | 00m00s
[101/115] expat-0:2.6.3-1.fc42.aarch64 100% | 9.1 MiB/s | 111.4 KiB | 00m00s
[102/115] mpdecimal-0:2.5.1-16.fc41.aar 100% | 43.5 MiB/s | 89.1 KiB | 00m00s
[103/115] tzdata-0:2024a-9.fc41.noarch 100% | 116.3 MiB/s | 714.7 KiB | 00m00s
[104/115] python-pip-wheel-0:24.2-2.fc4 100% | 133.5 MiB/s | 1.2 MiB | 00m00s
[105/115] perl-IO-Socket-IP-0:0.42-512. 100% | 6.8 MiB/s | 41.8 KiB | 00m00s
[106/115] perl-URI-0:5.29-1.fc42.noarch 100% | 44.8 MiB/s | 137.7 KiB | 00m00s
[107/115] perl-MIME-Base32-0:1.303-21.f 100% | 10.0 MiB/s | 20.5 KiB | 00m00s
[108/115] perl-AutoLoader-0:5.74-511.fc 100% | 10.4 MiB/s | 21.2 KiB | 00m00s
[109/115] perl-Digest-MD5-0:2.59-5.fc41 100% | 17.6 MiB/s | 36.1 KiB | 00m00s
[110/115] perl-libnet-0:3.15-512.fc41.n 100% | 31.4 MiB/s | 128.5 KiB | 00m00s
[111/115] perl-FileHandle-0:2.05-511.fc 100% | 3.8 MiB/s | 15.5 KiB | 00m00s
[112/115] perl-Digest-0:1.20-511.fc41.n 100% | 12.2 MiB/s | 24.9 KiB | 00m00s
[113/115] gcc-plugin-annobin-0:14.2.1-3 100% | 13.5 MiB/s | 55.2 KiB | 00m00s
[114/115] annobin-docs-0:12.70-1.fc42.n 100% | 22.5 MiB/s | 92.0 KiB | 00m00s
[115/115] annobin-plugin-gcc-0:12.70-1. 100% | 135.6 MiB/s | 972.0 KiB | 00m00s
--------------------------------------------------------------------------------
[115/115] Total 100% | 187.1 MiB/s | 75.4 MiB | 00m00s
Running transaction
[ 1/117] Verify package files 100% | 425.0 B/s | 115.0 B | 00m00s
[ 2/117] Prepare transaction 100% | 1.7 KiB/s | 115.0 B | 00m00s
[ 3/117] Installing htslib-0:1.15.1-6. 100% | 256.9 MiB/s | 1.8 MiB | 00m00s
[ 4/117] Installing libmpc-0:1.3.1-6.f 100% | 137.8 MiB/s | 282.3 KiB | 00m00s
[ 5/117] Installing cpp-0:14.2.1-3.fc4 100% | 289.0 MiB/s | 31.8 MiB | 00m00s
[ 6/117] Installing annobin-docs-0:12. 100% | 19.3 MiB/s | 98.8 KiB | 00m00s
[ 7/117] Installing tzdata-0:2024a-9.f 100% | 38.1 MiB/s | 1.9 MiB | 00m00s
[ 8/117] Installing python-pip-wheel-0 100% | 413.9 MiB/s | 1.2 MiB | 00m00s
[ 9/117] Installing mpdecimal-0:2.5.1- 100% | 161.1 MiB/s | 330.0 KiB | 00m00s
[ 10/117] Installing libb2-0:0.98.1-12. 100% | 198.6 MiB/s | 203.3 KiB | 00m00s
[ 11/117] Installing expat-0:2.6.3-1.fc 100% | 75.6 MiB/s | 541.7 KiB | 00m00s
[ 12/117] Installing python3-libs-0:3.1 100% | 277.1 MiB/s | 50.2 MiB | 00m00s
[ 13/117] Installing python3-0:3.13.0~r 100% | 208.6 MiB/s | 213.6 KiB | 00m00s
[ 14/117] Installing python3-pyparsing- 100% | 247.2 MiB/s | 1.0 MiB | 00m00s
[ 15/117] Installing systemtap-sdt-dtra 100% | 176.0 MiB/s | 180.2 KiB | 00m00s
[ 16/117] Installing ncurses-0:6.5-2.20 100% | 129.9 MiB/s | 1.7 MiB | 00m00s
[ 17/117] Installing groff-base-0:1.23. 100% | 179.3 MiB/s | 5.2 MiB | 00m00s
[ 18/117] Installing perl-Digest-0:1.20 100% | 36.2 MiB/s | 37.1 KiB | 00m00s
[ 19/117] Installing perl-B-0:1.89-511. 100% | 148.8 MiB/s | 609.4 KiB | 00m00s
[ 20/117] Installing perl-FileHandle-0: 100% | 9.5 MiB/s | 9.8 KiB | 00m00s
[ 21/117] Installing perl-Digest-MD5-0: 100% | 228.3 MiB/s | 233.8 KiB | 00m00s
[ 22/117] Installing perl-Data-Dumper-0 100% | 129.7 MiB/s | 265.7 KiB | 00m00s
[ 23/117] Installing perl-MIME-Base32-0 100% | 31.4 MiB/s | 32.2 KiB | 00m00s
[ 24/117] Installing perl-libnet-0:3.15 100% | 143.9 MiB/s | 294.7 KiB | 00m00s
[ 25/117] Installing perl-IO-Socket-IP- 100% | 98.1 MiB/s | 100.5 KiB | 00m00s
[ 26/117] Installing perl-AutoLoader-0: 100% | 20.5 MiB/s | 20.9 KiB | 00m00s
[ 27/117] Installing perl-URI-0:5.29-1. 100% | 64.4 MiB/s | 263.8 KiB | 00m00s
[ 28/117] Installing perl-Text-Tabs+Wra 100% | 23.3 MiB/s | 23.9 KiB | 00m00s
[ 29/117] Installing perl-File-Path-0:2 100% | 63.0 MiB/s | 64.5 KiB | 00m00s
[ 30/117] Installing perl-locale-0:1.12 100% | 0.0 B/s | 6.9 KiB | 00m00s
[ 31/117] Installing perl-Mozilla-CA-0: 100% | 10.6 MiB/s | 10.8 KiB | 00m00s
[ 32/117] Installing perl-Time-Local-2: 100% | 68.9 MiB/s | 70.6 KiB | 00m00s
[ 33/117] Installing perl-Pod-Escapes-1 100% | 25.3 MiB/s | 25.9 KiB | 00m00s
[ 34/117] Installing perl-if-0:0.61.000 100% | 6.1 MiB/s | 6.2 KiB | 00m00s
[ 35/117] Installing perl-Net-SSLeay-0: 100% | 179.1 MiB/s | 1.4 MiB | 00m00s
[ 36/117] Installing perl-IO-Socket-SSL 100% | 230.3 MiB/s | 707.4 KiB | 00m00s
[ 37/117] Installing perl-Class-Struct- 100% | 25.3 MiB/s | 25.9 KiB | 00m00s
[ 38/117] Installing perl-POSIX-0:2.20- 100% | 160.4 MiB/s | 328.5 KiB | 00m00s
[ 39/117] Installing perl-IPC-Open3-0:1 100% | 22.7 MiB/s | 23.3 KiB | 00m00s
[ 40/117] Installing perl-Term-ANSIColo 100% | 96.9 MiB/s | 99.2 KiB | 00m00s
[ 41/117] Installing perl-Term-Cap-0:1. 100% | 29.9 MiB/s | 30.6 KiB | 00m00s
[ 42/117] Installing perl-HTTP-Tiny-0:0 100% | 75.3 MiB/s | 154.2 KiB | 00m00s
[ 43/117] Installing perl-Pod-Simple-1: 100% | 139.3 MiB/s | 570.5 KiB | 00m00s
[ 44/117] Installing perl-File-Temp-1:0 100% | 80.1 MiB/s | 164.1 KiB | 00m00s
[ 45/117] Installing perl-Socket-4:2.03 100% | 133.9 MiB/s | 274.1 KiB | 00m00s
[ 46/117] Installing perl-SelectSaver-0 100% | 0.0 B/s | 2.6 KiB | 00m00s
[ 47/117] Installing perl-Symbol-0:1.09 100% | 0.0 B/s | 7.2 KiB | 00m00s
[ 48/117] Installing perl-File-stat-0:1 100% | 12.7 MiB/s | 13.1 KiB | 00m00s
[ 49/117] Installing perl-podlators-1:6 100% | 157.0 MiB/s | 321.4 KiB | 00m00s
[ 50/117] Installing perl-Pod-Perldoc-0 100% | 82.6 MiB/s | 169.3 KiB | 00m00s
[ 51/117] Installing perl-Fcntl-0:1.18- 100% | 217.0 MiB/s | 222.2 KiB | 00m00s
[ 52/117] Installing perl-Text-ParseWor 100% | 14.2 MiB/s | 14.6 KiB | 00m00s
[ 53/117] Installing perl-base-0:2.27-5 100% | 0.0 B/s | 12.9 KiB | 00m00s
[ 54/117] Installing perl-mro-0:1.29-51 100% | 205.9 MiB/s | 210.8 KiB | 00m00s
[ 55/117] Installing perl-IO-0:1.55-511 100% | 157.9 MiB/s | 323.4 KiB | 00m00s
[ 56/117] Installing perl-overloading-0 100% | 0.0 B/s | 5.5 KiB | 00m00s
[ 57/117] Installing perl-Pod-Usage-4:2 100% | 84.3 MiB/s | 86.3 KiB | 00m00s
[ 58/117] Installing perl-Errno-0:1.38- 100% | 0.0 B/s | 8.8 KiB | 00m00s
[ 59/117] Installing perl-Scalar-List-U 100% | 137.7 MiB/s | 282.0 KiB | 00m00s
[ 60/117] Installing perl-constant-0:1. 100% | 26.7 MiB/s | 27.4 KiB | 00m00s
[ 61/117] Installing perl-parent-1:0.24 100% | 0.0 B/s | 10.7 KiB | 00m00s
[ 62/117] Installing perl-File-Basename 100% | 0.0 B/s | 14.6 KiB | 00m00s
[ 63/117] Installing perl-vars-0:1.05-5 100% | 0.0 B/s | 4.3 KiB | 00m00s
[ 64/117] Installing perl-overload-0:1. 100% | 70.3 MiB/s | 71.9 KiB | 00m00s
[ 65/117] Installing perl-Getopt-Std-0: 100% | 0.0 B/s | 11.7 KiB | 00m00s
[ 66/117] Installing perl-MIME-Base64-0 100% | 219.2 MiB/s | 224.4 KiB | 00m00s
[ 67/117] Installing perl-Storable-1:3. 100% | 182.6 MiB/s | 374.1 KiB | 00m00s
[ 68/117] Installing perl-Getopt-Long-1 100% | 71.9 MiB/s | 147.2 KiB | 00m00s
[ 69/117] Installing perl-Exporter-0:5. 100% | 54.3 MiB/s | 55.6 KiB | 00m00s
[ 70/117] Installing perl-Carp-0:1.54-5 100% | 46.6 MiB/s | 47.7 KiB | 00m00s
[ 71/117] Installing perl-PathTools-0:3 100% | 174.1 MiB/s | 356.6 KiB | 00m00s
[ 72/117] Installing perl-DynaLoader-0: 100% | 31.7 MiB/s | 32.5 KiB | 00m00s
[ 73/117] Installing perl-Encode-4:3.21 100% | 295.3 MiB/s | 5.9 MiB | 00m00s
[ 74/117] Installing perl-libs-4:5.40.0 100% | 206.8 MiB/s | 11.0 MiB | 00m00s
[ 75/117] Installing perl-interpreter-4 100% | 296.9 MiB/s | 304.0 KiB | 00m00s
[ 76/117] Installing perl-File-Find-0:1 100% | 41.5 MiB/s | 42.5 KiB | 00m00s
[ 77/117] Installing perl-File-Copy-0:2 100% | 0.0 B/s | 20.2 KiB | 00m00s
[ 78/117] Installing perl-File-Compare- 100% | 0.0 B/s | 6.1 KiB | 00m00s
[ 79/117] Installing perl-ExtUtils-Pars 100% | 131.9 MiB/s | 405.1 KiB | 00m00s
[ 80/117] Installing perl-threads-1:2.4 100% | 129.5 MiB/s | 265.3 KiB | 00m00s
[ 81/117] Installing perl-threads-share 100% | 114.3 MiB/s | 234.0 KiB | 00m00s
[ 82/117] Installing perl-Thread-Queue- 100% | 29.7 MiB/s | 30.4 KiB | 00m00s
[ 83/117] Installing perl-ExtUtils-Comm 100% | 0.0 B/s | 10.2 KiB | 00m00s
[ 84/117] Installing perl-ExtUtils-Mani 100% | 84.3 MiB/s | 86.3 KiB | 00m00s
[ 85/117] Installing perl-Devel-PPPort- 100% | 319.9 MiB/s | 982.6 KiB | 00m00s
[ 86/117] Installing perl-ExtUtils-Cons 100% | 85.5 MiB/s | 87.6 KiB | 00m00s
[ 87/117] Installing perl-AutoSplit-0:5 100% | 23.0 MiB/s | 23.5 KiB | 00m00s
[ 88/117] Installing perl-lib-0:0.65-51 100% | 0.0 B/s | 8.9 KiB | 00m00s
[ 89/117] Installing perl-version-9:0.9 100% | 142.4 MiB/s | 291.7 KiB | 00m00s
[ 90/117] Installing perl-Benchmark-0:1 100% | 35.9 MiB/s | 36.7 KiB | 00m00s
[ 91/117] Installing perl-Test-Harness- 100% | 81.3 MiB/s | 582.4 KiB | 00m00s
[ 92/117] Installing perl-ExtUtils-Inst 100% | 85.1 MiB/s | 87.2 KiB | 00m00s
[ 93/117] Installing perl-ExtUtils-Make 100% | 145.5 MiB/s | 744.8 KiB | 00m00s
[ 94/117] Installing m4-0:1.4.19-10.fc4 100% | 131.8 MiB/s | 675.0 KiB | 00m00s
[ 95/117] Installing emacs-filesystem-1 100% | 531.2 KiB/s | 544.0 B | 00m00s
[ 96/117] Installing autoconf-0:2.72-3. 100% | 254.3 MiB/s | 2.8 MiB | 00m00s
[ 97/117] Installing automake-0:1.16.5- 100% | 196.0 MiB/s | 1.8 MiB | 00m00s
[ 98/117] Installing systemtap-sdt-deve 100% | 59.8 MiB/s | 183.8 KiB | 00m00s
[ 99/117] Installing kernel-headers-0:6 100% | 136.8 MiB/s | 6.4 MiB | 00m00s
[100/117] Installing libxcrypt-devel-0: 100% | 10.6 MiB/s | 32.6 KiB | 00m00s
[101/117] Installing glibc-devel-0:2.40 100% | 108.9 MiB/s | 2.3 MiB | 00m00s
[102/117] Installing perl-devel-4:5.40. 100% | 447.4 MiB/s | 8.1 MiB | 00m00s
[103/117] Installing cmake-filesystem-0 100% | 3.5 MiB/s | 7.1 KiB | 00m00s
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[105/117] Installing libubsan-0:14.2.1- 100% | 263.7 MiB/s | 540.1 KiB | 00m00s
[106/117] Installing libatomic-0:14.2.1 100% | 193.1 MiB/s | 197.8 KiB | 00m00s
[107/117] Installing libasan-0:14.2.1-3 100% | 320.5 MiB/s | 1.6 MiB | 00m00s
[108/117] Installing make-1:4.4.1-8.fc4 100% | 205.6 MiB/s | 1.9 MiB | 00m00s
[109/117] Installing gcc-0:14.2.1-3.fc4 100% | 316.9 MiB/s | 93.8 MiB | 00m00s
[110/117] Installing annobin-plugin-gcc 100% | 60.9 MiB/s | 1.1 MiB | 00m00s
[111/117] Installing gcc-plugin-annobin 100% | 10.2 MiB/s | 198.7 KiB | 00m00s
[112/117] Installing gsl-devel-0:2.7.1- 100% | 137.7 MiB/s | 1.7 MiB | 00m00s
[113/117] Installing zlib-ng-compat-dev 100% | 105.8 MiB/s | 108.3 KiB | 00m00s
[114/117] Installing perl-ExtUtils-Embe 100% | 15.7 MiB/s | 16.1 KiB | 00m00s
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[116/117] Installing htslib-devel-0:1.1 100% | 202.9 MiB/s | 415.5 KiB | 00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
[117/117] Installing htslib-tools-0:1.1 100% | 11.8 MiB/s | 2.5 MiB | 00m00s
Warning: skipped PGP checks for 1 package from repository: copr_base
Complete!
Finish: build setup for bcftools-1.15.1-10.fc42.src.rpm
Start: rpmbuild bcftools-1.15.1-10.fc42.src.rpm
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1721174400
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.E8qlPp
+ umask 022
+ cd /builddir/build/BUILD/bcftools-1.15.1-build
+ test -d /builddir/build/BUILD/bcftools-1.15.1-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/bcftools-1.15.1-build
+ /usr/bin/rm -rf /builddir/build/BUILD/bcftools-1.15.1-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build/SPECPARTS
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.8kVPbW
+ umask 022
+ cd /builddir/build/BUILD/bcftools-1.15.1-build
+ cd /builddir/build/BUILD/bcftools-1.15.1-build
+ rm -rf bcftools-1.15.1
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/bcftools-1.15.1.tar.bz2
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd bcftools-1.15.1
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ echo 'Patch #0 (bcftools-1.15.1-aarch64-fix-vcf_plugin-tests.patch):'
Patch #0 (bcftools-1.15.1-aarch64-fix-vcf_plugin-tests.patch):
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0
patching file plugins/fill-tags.c
+ 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.ihQxUh
+ umask 022
+ cd /builddir/build/BUILD/bcftools-1.15.1-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bcftools-1.15.1
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ 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' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
--- ./htslib-1.15.1/configure.backup 2022-04-07 15:42:52.000000000 +0000
+++ ./htslib-1.15.1/configure 2024-09-25 14:26:49.775632695 +0000
@@ -1697,7 +1697,7 @@
#ifdef __cplusplus
extern "C"
#endif
-char $2 ();
+__attribute__ ((used)) char $2 ();
/* The GNU C library defines this for functions which it implements
to always fail with ENOSYS. Some functions are actually named
something starting with __ and the normal name is an alias. */
+ /usr/bin/sed --in-place=.backup '1{$!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-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/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-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/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' ./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
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
++ echo --runstatedir=/run
+ ./configure --build=aarch64-redhat-linux --host=aarch64-redhat-linux --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 --runstatedir=/run --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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --with-htslib=system --enable-perl-filters --enable-libgsl '--with-bcf-plugin-path=/usr/local/libexec/bcftools:$(plugindir)'
checking for aarch64-redhat-linux-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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
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
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 -j4 V=1 VERBOSE=1
echo '#define BCFTOOLS_VERSION "1.15.1"' > version.h
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o tabix.o tabix.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfindex.o vcfindex.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfisec.o vcfisec.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfquery.o vcfquery.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcffilter.o vcffilter.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfstats.o vcfstats.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfsom.o vcfsom.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfgtcheck.o vcfgtcheck.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfview.o vcfview.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfmerge.o vcfmerge.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfnorm.o vcfnorm.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfroh.o vcfroh.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfconcat.o vcfconcat.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcmp.o vcmp.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o gvcf.o gvcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfcall.o vcfcall.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o mcall.o mcall.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfannotate.o vcfannotate.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o reheader.o reheader.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o tsv2vcf.o tsv2vcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfhead.o vcfhead.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o HMM.o HMM.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfcnv.o vcfcnv.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfconvert.o vcfconvert.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o ploidy.o ploidy.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o bin.o bin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o convert.o convert.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o version.o version.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o hclust.o hclust.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o consensus.o consensus.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o smpl_ilist.o smpl_ilist.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o regidx.o regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfbuf.o vcfbuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o mpileup.o mpileup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o bam2bcf.o bam2bcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o cols.o cols.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfsort.o vcfsort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o dist.o dist.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o extsort.o extsort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o bam_sample.o bam_sample.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o em.o em.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o ccall.o ccall.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o kmin.o kmin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o str_finder.o str_finder.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o prob1.o prob1.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o abuf.o abuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o polysomy.o polysomy.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o peakfit.o peakfit.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/GTsubset.so version.c plugins/GTsubset.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o csq.o csq.c
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/mendelian.so version.c plugins/mendelian.c
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/test-rbuf test/test-rbuf.o -lz
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-stats.so version.c plugins/trio-stats.c
gcc -rdynamic -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o polysomy.o peakfit.o vcfplugin.o -lhts -lm -lz -lgsl -lgslcblas -Wl,--enable-new-dtags -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -fstack-protector-strong -L/usr/local/lib -L/usr/lib64/perl5/CORE -lperl -lpthread -lresolv -ldl -lm -lcrypt -lutil -lc -lpthread
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.ZPga8d
+ umask 022
+ cd /builddir/build/BUILD/bcftools-1.15.1-build
+ '[' /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT
++ dirname /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build
+ mkdir /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bcftools-1.15.1
+ /usr/bin/make install DESTDIR=/builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/bin /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/man/man1 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/libexec/bcftools
/usr/bin/install -p bcftools /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/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/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/bin
/usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/man/man1
/usr/bin/install -p plugins/*.so /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/libexec/bcftools
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.15.1-10.fc42 --unique-debug-suffix -1.15.1-10.fc42.aarch64 --unique-debug-src-base bcftools-1.15.1-10.fc42.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1
find-debuginfo: starting
Extracting debug info from 39 files
DWARF-compressing 39 files
sepdebugcrcfix: Updated 39 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/bcftools-1.15.1-10.fc42.aarch64
5400 blocks
find-debuginfo: done
+ /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/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-determinism --brp -j4 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT
Scanned 19 directories and 208 files,
processed 0 inodes,
0 modified (0 replaced + 0 rewritten),
0 unsupported format, 0 errors
Reading /builddir/build/BUILD/bcftools-1.15.1-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.u4PIYq
+ umask 022
+ cd /builddir/build/BUILD/bcftools-1.15.1-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bcftools-1.15.1
+ ldd bcftools
+ grep -E '/lib(64)?/libhts\.so\.'
libhts.so.3 => /lib64/libhts.so.3 (0x0000ffff82bd0000)
+ 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/z7I5WgpJtN/merge.a.vcf.gz 2:3199812-3199812
.. ok
test_tabix:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/z7I5WgpJtN/merge.a.bcf 2:3199812-3199812
.. ok
test_tabix:
tabix /tmp/z7I5WgpJtN/merge.a.vcf.gz 1:3000151-3000151
.. ok
test_tabix:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/z7I5WgpJtN/merge.a.bcf 1:3000151-3000151
.. ok
test_index:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/z7I5WgpJtN/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
.. ok
test_index:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/z7I5WgpJtN/large_chrom_csi_limit.bcf chr20:1-2147483647
.. ok
test_index:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/z7I5WgpJtN/large_chrom_csi_limit.bcf chr20:1-2147483647
.. ok
test_index:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/z7I5WgpJtN/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
.. ok
test_index:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/z7I5WgpJtN/large_chrom_csi_limit.bcf chr20:1-2147483647
.. ok
test_index:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/z7I5WgpJtN/large_chrom_csi_limit.vcf.gz chr20
.. ok
test_index:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/z7I5WgpJtN/large_chrom_csi_limit.bcf chr20
.. ok
test_index:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/z7I5WgpJtN/large_chrom_csi_limit.bcf chr20
.. ok
test_index:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/z7I5WgpJtN/large_chrom_csi_limit.vcf.gz chr20
.. ok
test_index:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/z7I5WgpJtN/large_chrom_csi_limit.bcf chr20
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/z7I5WgpJtN/idx.vcf.gz
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/z7I5WgpJtN/idx.vcf.gz
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/z7I5WgpJtN/idx.bcf
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/z7I5WgpJtN/idx.vcf.gz
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/z7I5WgpJtN/idx.vcf.gz
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/z7I5WgpJtN/idx.vcf.gz.csi
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/z7I5WgpJtN/idx.bcf
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/z7I5WgpJtN/idx.bcf.csi
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/z7I5WgpJtN/empty.vcf.gz
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/z7I5WgpJtN/empty.vcf.gz
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/z7I5WgpJtN/empty.bcf
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/z7I5WgpJtN/empty.vcf.gz
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/z7I5WgpJtN/empty.vcf.gz
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/z7I5WgpJtN/empty.vcf.gz.csi
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/z7I5WgpJtN/empty.bcf
.. ok
test_vcf_idxstats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/z7I5WgpJtN/empty.bcf.csi
.. ok
test_vcf_check:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s - /tmp/z7I5WgpJtN/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
.. ok
test_vcf_check:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
.. ok
test_vcf_check_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/misc/plot-vcfstats -m /tmp/z7I5WgpJtN/check.1.chk /tmp/z7I5WgpJtN/check.2.chk /tmp/z7I5WgpJtN/check.3.chk /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools stats -s - /tmp/z7I5WgpJtN/stats.a.vcf.gz /tmp/z7I5WgpJtN/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
.. ok
test_vcf_stats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s B /tmp/z7I5WgpJtN/stats.a.vcf.gz /tmp/z7I5WgpJtN/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
.. ok
test_vcf_stats:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s - /tmp/z7I5WgpJtN/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID '
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n =2 /tmp/z7I5WgpJtN/isec.a.vcf.gz /tmp/z7I5WgpJtN/isec.b.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n =2 /tmp/z7I5WgpJtN/isec.a.vcf.gz /tmp/z7I5WgpJtN/isec.b.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/z7I5WgpJtN/isec.a.vcf.gz /tmp/z7I5WgpJtN/isec.b.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/z7I5WgpJtN/isec.a.vcf.gz /tmp/z7I5WgpJtN/isec.b.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n =2 -c both /tmp/z7I5WgpJtN/isec.a.vcf.gz /tmp/z7I5WgpJtN/isec.b.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n =2 -c both /tmp/z7I5WgpJtN/isec.a.vcf.gz /tmp/z7I5WgpJtN/isec.b.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n =2 -c any /tmp/z7I5WgpJtN/isec.a.vcf.gz /tmp/z7I5WgpJtN/isec.b.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n =2 -c any /tmp/z7I5WgpJtN/isec.a.vcf.gz /tmp/z7I5WgpJtN/isec.b.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -C -c any /tmp/z7I5WgpJtN/isec.a.vcf.gz /tmp/z7I5WgpJtN/isec.b.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -C -c any /tmp/z7I5WgpJtN/isec.a.vcf.gz /tmp/z7I5WgpJtN/isec.b.vcf.gz
.. ok
test_vcf_isec2:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec --no-version -T /tmp/z7I5WgpJtN/isec.tab.gz /tmp/z7I5WgpJtN/isec.a.vcf.gz
.. ok
test_vcf_isec2:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -T /tmp/z7I5WgpJtN/isec.tab.gz /tmp/z7I5WgpJtN/isec.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/z7I5WgpJtN/isec-miss.1.1.vcf.gz /tmp/z7I5WgpJtN/isec-miss.1.2.vcf.gz /tmp/z7I5WgpJtN/isec-miss.1.3.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/z7I5WgpJtN/isec-miss.1.1.vcf.gz /tmp/z7I5WgpJtN/isec-miss.1.2.vcf.gz /tmp/z7I5WgpJtN/isec-miss.1.3.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/z7I5WgpJtN/isec-miss.1.1.vcf.gz /tmp/z7I5WgpJtN/isec-miss.1.2.vcf.gz /tmp/z7I5WgpJtN/isec-miss.1.3.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/z7I5WgpJtN/isec-miss.1.1.vcf.gz /tmp/z7I5WgpJtN/isec-miss.1.2.vcf.gz /tmp/z7I5WgpJtN/isec-miss.1.3.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/z7I5WgpJtN/isec-miss.2.1.vcf.gz /tmp/z7I5WgpJtN/isec-miss.2.2.vcf.gz /tmp/z7I5WgpJtN/isec-miss.2.3.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/z7I5WgpJtN/isec-miss.2.1.vcf.gz /tmp/z7I5WgpJtN/isec-miss.2.2.vcf.gz /tmp/z7I5WgpJtN/isec-miss.2.3.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/z7I5WgpJtN/isec-miss.2.1.vcf.gz /tmp/z7I5WgpJtN/isec-miss.2.2.vcf.gz /tmp/z7I5WgpJtN/isec-miss.2.3.vcf.gz
.. ok
test_vcf_isec:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/z7I5WgpJtN/isec-miss.2.1.vcf.gz /tmp/z7I5WgpJtN/isec-miss.2.2.vcf.gz /tmp/z7I5WgpJtN/isec-miss.2.3.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AF:join /tmp/z7I5WgpJtN/merge.join.a.vcf.gz /tmp/z7I5WgpJtN/merge.join.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AF:join /tmp/z7I5WgpJtN/merge.join.a.vcf.gz /tmp/z7I5WgpJtN/merge.join.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AF:join /tmp/z7I5WgpJtN/merge.join.a.bcf /tmp/z7I5WgpJtN/merge.join.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AF:join /tmp/z7I5WgpJtN/merge.join.a.bcf /tmp/z7I5WgpJtN/merge.join.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/z7I5WgpJtN/merge.LPL.a.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.b.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.c.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/z7I5WgpJtN/merge.LPL.a.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.b.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/z7I5WgpJtN/merge.LPL.a.bcf /tmp/z7I5WgpJtN/merge.LPL.b.bcf /tmp/z7I5WgpJtN/merge.LPL.c.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/z7I5WgpJtN/merge.LPL.a.bcf /tmp/z7I5WgpJtN/merge.LPL.b.bcf /tmp/z7I5WgpJtN/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 1 /tmp/z7I5WgpJtN/merge.LPL.a.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.b.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.c.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 1 /tmp/z7I5WgpJtN/merge.LPL.a.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.b.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 1 /tmp/z7I5WgpJtN/merge.LPL.a.bcf /tmp/z7I5WgpJtN/merge.LPL.b.bcf /tmp/z7I5WgpJtN/merge.LPL.c.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 1 /tmp/z7I5WgpJtN/merge.LPL.a.bcf /tmp/z7I5WgpJtN/merge.LPL.b.bcf /tmp/z7I5WgpJtN/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 2 /tmp/z7I5WgpJtN/merge.LPL.a.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.b.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.c.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 2 /tmp/z7I5WgpJtN/merge.LPL.a.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.b.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 2 /tmp/z7I5WgpJtN/merge.LPL.a.bcf /tmp/z7I5WgpJtN/merge.LPL.b.bcf /tmp/z7I5WgpJtN/merge.LPL.c.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 2 /tmp/z7I5WgpJtN/merge.LPL.a.bcf /tmp/z7I5WgpJtN/merge.LPL.b.bcf /tmp/z7I5WgpJtN/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 3 /tmp/z7I5WgpJtN/merge.LPL.a.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.b.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.c.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 3 /tmp/z7I5WgpJtN/merge.LPL.a.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.b.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 3 /tmp/z7I5WgpJtN/merge.LPL.a.bcf /tmp/z7I5WgpJtN/merge.LPL.b.bcf /tmp/z7I5WgpJtN/merge.LPL.c.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 3 /tmp/z7I5WgpJtN/merge.LPL.a.bcf /tmp/z7I5WgpJtN/merge.LPL.b.bcf /tmp/z7I5WgpJtN/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 4 /tmp/z7I5WgpJtN/merge.LPL.a.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.b.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.c.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 4 /tmp/z7I5WgpJtN/merge.LPL.a.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.b.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 4 /tmp/z7I5WgpJtN/merge.LPL.a.bcf /tmp/z7I5WgpJtN/merge.LPL.b.bcf /tmp/z7I5WgpJtN/merge.LPL.c.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 4 /tmp/z7I5WgpJtN/merge.LPL.a.bcf /tmp/z7I5WgpJtN/merge.LPL.b.bcf /tmp/z7I5WgpJtN/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 5 /tmp/z7I5WgpJtN/merge.LPL.a.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.b.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.c.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 5 /tmp/z7I5WgpJtN/merge.LPL.a.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.b.vcf.gz /tmp/z7I5WgpJtN/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 5 /tmp/z7I5WgpJtN/merge.LPL.a.bcf /tmp/z7I5WgpJtN/merge.LPL.b.bcf /tmp/z7I5WgpJtN/merge.LPL.c.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 5 /tmp/z7I5WgpJtN/merge.LPL.a.bcf /tmp/z7I5WgpJtN/merge.LPL.b.bcf /tmp/z7I5WgpJtN/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/z7I5WgpJtN/merge.a.vcf.gz /tmp/z7I5WgpJtN/merge.b.vcf.gz /tmp/z7I5WgpJtN/merge.c.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/z7I5WgpJtN/merge.a.vcf.gz /tmp/z7I5WgpJtN/merge.b.vcf.gz /tmp/z7I5WgpJtN/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/z7I5WgpJtN/merge.a.bcf /tmp/z7I5WgpJtN/merge.b.bcf /tmp/z7I5WgpJtN/merge.c.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/z7I5WgpJtN/merge.a.bcf /tmp/z7I5WgpJtN/merge.b.bcf /tmp/z7I5WgpJtN/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -Fx /tmp/z7I5WgpJtN/merge.a.vcf.gz /tmp/z7I5WgpJtN/merge.b.vcf.gz /tmp/z7I5WgpJtN/merge.c.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -Fx /tmp/z7I5WgpJtN/merge.a.vcf.gz /tmp/z7I5WgpJtN/merge.b.vcf.gz /tmp/z7I5WgpJtN/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -Fx /tmp/z7I5WgpJtN/merge.a.bcf /tmp/z7I5WgpJtN/merge.b.bcf /tmp/z7I5WgpJtN/merge.c.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -Fx /tmp/z7I5WgpJtN/merge.a.bcf /tmp/z7I5WgpJtN/merge.b.bcf /tmp/z7I5WgpJtN/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -0 /tmp/z7I5WgpJtN/merge.a.vcf.gz /tmp/z7I5WgpJtN/merge.b.vcf.gz /tmp/z7I5WgpJtN/merge.c.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -0 /tmp/z7I5WgpJtN/merge.a.vcf.gz /tmp/z7I5WgpJtN/merge.b.vcf.gz /tmp/z7I5WgpJtN/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -0 /tmp/z7I5WgpJtN/merge.a.bcf /tmp/z7I5WgpJtN/merge.b.bcf /tmp/z7I5WgpJtN/merge.c.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -0 /tmp/z7I5WgpJtN/merge.a.bcf /tmp/z7I5WgpJtN/merge.b.bcf /tmp/z7I5WgpJtN/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m none /tmp/z7I5WgpJtN/merge.2.a.vcf.gz /tmp/z7I5WgpJtN/merge.2.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m none /tmp/z7I5WgpJtN/merge.2.a.vcf.gz /tmp/z7I5WgpJtN/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m none /tmp/z7I5WgpJtN/merge.2.a.bcf /tmp/z7I5WgpJtN/merge.2.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m none /tmp/z7I5WgpJtN/merge.2.a.bcf /tmp/z7I5WgpJtN/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m both /tmp/z7I5WgpJtN/merge.2.a.vcf.gz /tmp/z7I5WgpJtN/merge.2.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m both /tmp/z7I5WgpJtN/merge.2.a.vcf.gz /tmp/z7I5WgpJtN/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m both /tmp/z7I5WgpJtN/merge.2.a.bcf /tmp/z7I5WgpJtN/merge.2.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m both /tmp/z7I5WgpJtN/merge.2.a.bcf /tmp/z7I5WgpJtN/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m all /tmp/z7I5WgpJtN/merge.2.a.vcf.gz /tmp/z7I5WgpJtN/merge.2.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m all /tmp/z7I5WgpJtN/merge.2.a.vcf.gz /tmp/z7I5WgpJtN/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m all /tmp/z7I5WgpJtN/merge.2.a.bcf /tmp/z7I5WgpJtN/merge.2.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m all /tmp/z7I5WgpJtN/merge.2.a.bcf /tmp/z7I5WgpJtN/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/z7I5WgpJtN/merge.3.a.vcf.gz /tmp/z7I5WgpJtN/merge.3.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/z7I5WgpJtN/merge.3.a.vcf.gz /tmp/z7I5WgpJtN/merge.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/z7I5WgpJtN/merge.3.a.bcf /tmp/z7I5WgpJtN/merge.3.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/z7I5WgpJtN/merge.3.a.bcf /tmp/z7I5WgpJtN/merge.3.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m id /tmp/z7I5WgpJtN/merge.4.a.vcf.gz /tmp/z7I5WgpJtN/merge.4.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m id /tmp/z7I5WgpJtN/merge.4.a.vcf.gz /tmp/z7I5WgpJtN/merge.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m id /tmp/z7I5WgpJtN/merge.4.a.bcf /tmp/z7I5WgpJtN/merge.4.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m id /tmp/z7I5WgpJtN/merge.4.a.bcf /tmp/z7I5WgpJtN/merge.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/z7I5WgpJtN/gvcf.merge.1.vcf.gz /tmp/z7I5WgpJtN/gvcf.merge.2.vcf.gz /tmp/z7I5WgpJtN/gvcf.merge.3.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/z7I5WgpJtN/gvcf.merge.1.vcf.gz /tmp/z7I5WgpJtN/gvcf.merge.2.vcf.gz /tmp/z7I5WgpJtN/gvcf.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/z7I5WgpJtN/gvcf.merge.1.bcf /tmp/z7I5WgpJtN/gvcf.merge.2.bcf /tmp/z7I5WgpJtN/gvcf.merge.3.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/z7I5WgpJtN/gvcf.merge.1.bcf /tmp/z7I5WgpJtN/gvcf.merge.2.bcf /tmp/z7I5WgpJtN/gvcf.merge.3.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.2.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.2.b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.2.c.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.2.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.2.b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - -i SRC:join /tmp/z7I5WgpJtN/merge.gvcf.3.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.3.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - -i SRC:join /tmp/z7I5WgpJtN/merge.gvcf.3.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.4.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.4.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.4.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.4.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.4.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.4.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/z7I5WgpJtN/merge.5.a.vcf.gz /tmp/z7I5WgpJtN/merge.5.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/z7I5WgpJtN/merge.5.a.vcf.gz /tmp/z7I5WgpJtN/merge.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/z7I5WgpJtN/merge.5.a.bcf /tmp/z7I5WgpJtN/merge.5.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/z7I5WgpJtN/merge.5.a.bcf /tmp/z7I5WgpJtN/merge.5.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/z7I5WgpJtN/merge.6.a.vcf.gz /tmp/z7I5WgpJtN/merge.6.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/z7I5WgpJtN/merge.6.a.vcf.gz /tmp/z7I5WgpJtN/merge.6.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/z7I5WgpJtN/merge.6.a.bcf /tmp/z7I5WgpJtN/merge.6.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/z7I5WgpJtN/merge.6.a.bcf /tmp/z7I5WgpJtN/merge.6.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.7.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.7.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.7.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.7.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.7.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.7.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.7.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.8.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.8.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.8.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.8.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.8.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/z7I5WgpJtN/merge.gvcf.8.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/z7I5WgpJtN/merge.7.a.vcf.gz /tmp/z7I5WgpJtN/merge.7.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/z7I5WgpJtN/merge.7.a.vcf.gz /tmp/z7I5WgpJtN/merge.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/z7I5WgpJtN/merge.7.a.bcf /tmp/z7I5WgpJtN/merge.7.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/z7I5WgpJtN/merge.7.a.bcf /tmp/z7I5WgpJtN/merge.7.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/z7I5WgpJtN/merge.gvcf.9a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9c.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9d.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/z7I5WgpJtN/merge.gvcf.9a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9c.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/z7I5WgpJtN/merge.gvcf.9a.bcf /tmp/z7I5WgpJtN/merge.gvcf.9b.bcf /tmp/z7I5WgpJtN/merge.gvcf.9c.bcf /tmp/z7I5WgpJtN/merge.gvcf.9d.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/z7I5WgpJtN/merge.gvcf.9a.bcf /tmp/z7I5WgpJtN/merge.gvcf.9b.bcf /tmp/z7I5WgpJtN/merge.gvcf.9c.bcf /tmp/z7I5WgpJtN/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/z7I5WgpJtN/merge.gvcf.9a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9c.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9d.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/z7I5WgpJtN/merge.gvcf.9a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9c.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/z7I5WgpJtN/merge.gvcf.9a.bcf /tmp/z7I5WgpJtN/merge.gvcf.9b.bcf /tmp/z7I5WgpJtN/merge.gvcf.9c.bcf /tmp/z7I5WgpJtN/merge.gvcf.9d.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/z7I5WgpJtN/merge.gvcf.9a.bcf /tmp/z7I5WgpJtN/merge.gvcf.9b.bcf /tmp/z7I5WgpJtN/merge.gvcf.9c.bcf /tmp/z7I5WgpJtN/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/z7I5WgpJtN/merge.gvcf.9a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9c.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9d.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9e.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/z7I5WgpJtN/merge.gvcf.9a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9c.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9d.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/z7I5WgpJtN/merge.gvcf.9a.bcf /tmp/z7I5WgpJtN/merge.gvcf.9b.bcf /tmp/z7I5WgpJtN/merge.gvcf.9c.bcf /tmp/z7I5WgpJtN/merge.gvcf.9d.bcf /tmp/z7I5WgpJtN/merge.gvcf.9e.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/z7I5WgpJtN/merge.gvcf.9a.bcf /tmp/z7I5WgpJtN/merge.gvcf.9b.bcf /tmp/z7I5WgpJtN/merge.gvcf.9c.bcf /tmp/z7I5WgpJtN/merge.gvcf.9d.bcf /tmp/z7I5WgpJtN/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/z7I5WgpJtN/merge.gvcf.9a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9c.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9d.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9e.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/z7I5WgpJtN/merge.gvcf.9a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9c.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9d.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/z7I5WgpJtN/merge.gvcf.9a.bcf /tmp/z7I5WgpJtN/merge.gvcf.9b.bcf /tmp/z7I5WgpJtN/merge.gvcf.9c.bcf /tmp/z7I5WgpJtN/merge.gvcf.9d.bcf /tmp/z7I5WgpJtN/merge.gvcf.9e.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/z7I5WgpJtN/merge.gvcf.9a.bcf /tmp/z7I5WgpJtN/merge.gvcf.9b.bcf /tmp/z7I5WgpJtN/merge.gvcf.9c.bcf /tmp/z7I5WgpJtN/merge.gvcf.9d.bcf /tmp/z7I5WgpJtN/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/z7I5WgpJtN/merge.gvcf.10.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.10.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/z7I5WgpJtN/merge.gvcf.10.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/z7I5WgpJtN/merge.gvcf.10.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.10.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/z7I5WgpJtN/merge.gvcf.10.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -m none /tmp/z7I5WgpJtN/merge.gvcf.10.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.10.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -m none /tmp/z7I5WgpJtN/merge.gvcf.10.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -m none /tmp/z7I5WgpJtN/merge.gvcf.10.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.10.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -m none /tmp/z7I5WgpJtN/merge.gvcf.10.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/z7I5WgpJtN/merge.gvcf.10.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.10.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/z7I5WgpJtN/merge.gvcf.10.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/z7I5WgpJtN/merge.gvcf.10.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.10.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/z7I5WgpJtN/merge.gvcf.10.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/z7I5WgpJtN/merge.gvcf.10.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.10.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/z7I5WgpJtN/merge.gvcf.10.a.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/z7I5WgpJtN/merge.gvcf.10.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.10.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/z7I5WgpJtN/merge.gvcf.10.a.bcf /tmp/z7I5WgpJtN/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/z7I5WgpJtN/merge.gvcf.10.b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.10.a.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/z7I5WgpJtN/merge.gvcf.10.b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/z7I5WgpJtN/merge.gvcf.10.b.bcf /tmp/z7I5WgpJtN/merge.gvcf.10.a.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/z7I5WgpJtN/merge.gvcf.10.b.bcf /tmp/z7I5WgpJtN/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/z7I5WgpJtN/merge.gvcf.10.b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.10.a.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/z7I5WgpJtN/merge.gvcf.10.b.vcf.gz /tmp/z7I5WgpJtN/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/z7I5WgpJtN/merge.gvcf.10.b.bcf /tmp/z7I5WgpJtN/merge.gvcf.10.a.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/z7I5WgpJtN/merge.gvcf.10.b.bcf /tmp/z7I5WgpJtN/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/z7I5WgpJtN/merge.noidx.a.vcf.gz /tmp/z7I5WgpJtN/merge.noidx.b.vcf.gz /tmp/z7I5WgpJtN/merge.noidx.c.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/z7I5WgpJtN/merge.noidx.a.vcf.gz /tmp/z7I5WgpJtN/merge.noidx.b.vcf.gz /tmp/z7I5WgpJtN/merge.noidx.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/z7I5WgpJtN/merge.noidx.a.bcf /tmp/z7I5WgpJtN/merge.noidx.b.bcf /tmp/z7I5WgpJtN/merge.noidx.c.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/z7I5WgpJtN/merge.noidx.a.bcf /tmp/z7I5WgpJtN/merge.noidx.b.bcf /tmp/z7I5WgpJtN/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --no-index /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.c.vcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --no-index /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.c.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --no-index /tmp/z7I5WgpJtN/merge.noidx.a.bcf /tmp/z7I5WgpJtN/merge.noidx.b.bcf /tmp/z7I5WgpJtN/merge.noidx.c.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --no-index /tmp/z7I5WgpJtN/merge.noidx.a.bcf /tmp/z7I5WgpJtN/merge.noidx.b.bcf /tmp/z7I5WgpJtN/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/z7I5WgpJtN/merge.8.a.vcf.gz /tmp/z7I5WgpJtN/merge.8.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/z7I5WgpJtN/merge.8.a.vcf.gz /tmp/z7I5WgpJtN/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/z7I5WgpJtN/merge.8.a.bcf /tmp/z7I5WgpJtN/merge.8.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/z7I5WgpJtN/merge.8.a.bcf /tmp/z7I5WgpJtN/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/z7I5WgpJtN/merge.8.a.vcf.gz /tmp/z7I5WgpJtN/merge.8.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/z7I5WgpJtN/merge.8.a.vcf.gz /tmp/z7I5WgpJtN/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/z7I5WgpJtN/merge.8.a.bcf /tmp/z7I5WgpJtN/merge.8.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/z7I5WgpJtN/merge.8.a.bcf /tmp/z7I5WgpJtN/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/z7I5WgpJtN/merge.9.a.vcf.gz /tmp/z7I5WgpJtN/merge.9.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/z7I5WgpJtN/merge.9.a.vcf.gz /tmp/z7I5WgpJtN/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/z7I5WgpJtN/merge.9.a.bcf /tmp/z7I5WgpJtN/merge.9.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/z7I5WgpJtN/merge.9.a.bcf /tmp/z7I5WgpJtN/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/z7I5WgpJtN/merge.9.a.vcf.gz /tmp/z7I5WgpJtN/merge.9.b.vcf.gz
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/z7I5WgpJtN/merge.9.a.vcf.gz /tmp/z7I5WgpJtN/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/z7I5WgpJtN/merge.9.a.bcf /tmp/z7I5WgpJtN/merge.9.b.bcf
.. ok
test_vcf_merge:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/z7I5WgpJtN/merge.9.a.bcf /tmp/z7I5WgpJtN/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/z7I5WgpJtN/query.string.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/z7I5WgpJtN/query.string.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/z7I5WgpJtN/query.string.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools query -f '%RSX\t%VKX\n' /tmp/z7I5WgpJtN/query.variantkey.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.variantkey.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%RSX\t%VKX\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XRI\n' -i'XRI[*]>1111'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XRF\n' -i'XRF[*]=2e6'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[2]~"H"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]~"H"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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/z7I5WgpJtN/view.vectors.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/z7I5WgpJtN/query.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/z7I5WgpJtN/query.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/z7I5WgpJtN/query.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/z7I5WgpJtN/query.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/z7I5WgpJtN/query.2.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IINT="."' -f'%POS %IINT\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IINT!="."' -f'%POS %IINT\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IINT!="."' -f'%POS %IINT\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IINT="."' -f'%POS %IINT\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IFLT="."' -f'%POS %IFLT\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IFLT="."' -f'%POS %IFLT\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'ISTR="."' -f'%POS %ISTR\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'ISTR="."' -f'%POS %ISTR\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/z7I5WgpJtN/filter.11.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/z7I5WgpJtN/filter.11.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/z7I5WgpJtN/filter.11.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/z7I5WgpJtN/filter.11.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%LINE' /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%LINE'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/z7I5WgpJtN/query.filter-type.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/z7I5WgpJtN/query.filter-type.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/z7I5WgpJtN/query.filter-type.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/z7I5WgpJtN/query.filter-type.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/z7I5WgpJtN/query.filter-type.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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/z7I5WgpJtN/filter-missing-floats.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/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/z7I5WgpJtN/filter-missing-floats.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/z7I5WgpJtN/missing.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/z7I5WgpJtN/query.filter.2.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/z7I5WgpJtN/filter.5.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/z7I5WgpJtN/filter.5.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/z7I5WgpJtN/query.filter.3.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/z7I5WgpJtN/query.filter.3.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/z7I5WgpJtN/query.filter.3.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/z7I5WgpJtN/filter.5.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/z7I5WgpJtN/query.filter.4.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.56.out' /tmp/z7I5WgpJtN/view.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.56.out'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/z7I5WgpJtN/query.filter.5.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/z7I5WgpJtN/query.filter.5.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/z7I5WgpJtN/query.filter.5.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/z7I5WgpJtN/query.negative.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/z7I5WgpJtN/query.negative.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/z7I5WgpJtN/query.negative.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/z7I5WgpJtN/query.negative.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/z7I5WgpJtN/query.filter.11.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/z7I5WgpJtN/query.filter.11.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/z7I5WgpJtN/query.filter.11.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/z7I5WgpJtN/query.filter.11.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' /tmp/z7I5WgpJtN/query.pbinom.1.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.pbinom.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/z7I5WgpJtN/query.filter.6.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.6.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/z7I5WgpJtN/query.filter.7.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/z7I5WgpJtN/query.filter.7.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/z7I5WgpJtN/query.filter.7.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/z7I5WgpJtN/query.filter.7.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/z7I5WgpJtN/query.filter.7.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/z7I5WgpJtN/query.filter.7.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/z7I5WgpJtN/query.filter.7.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/z7I5WgpJtN/query.filter.7.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/z7I5WgpJtN/query.filter.8.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/z7I5WgpJtN/query.filter.8.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/z7I5WgpJtN/query.filter.9.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/z7I5WgpJtN/query.filter.9.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/z7I5WgpJtN/query.filter.13.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.13.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/z7I5WgpJtN/query.filter.10.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/z7I5WgpJtN/query.filter.10.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/z7I5WgpJtN/query.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/z7I5WgpJtN/query.filter.12.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/z7I5WgpJtN/query.filter.12.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt /tmp/z7I5WgpJtN/query.smpl.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt /tmp/z7I5WgpJtN/query.smpl.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt /tmp/z7I5WgpJtN/query.smpl.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt /tmp/z7I5WgpJtN/query.smpl.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.txt /tmp/z7I5WgpJtN/query.smpl.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.txt
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.txt /tmp/z7I5WgpJtN/query.smpl.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.txt
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/z7I5WgpJtN/query.filter.id.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID~"s12"'
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/z7I5WgpJtN/query.filter.id.vcf.gz
.. ok
test_vcf_query:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID="rs123"'
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -cx -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/z7I5WgpJtN/norm.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -cx -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/z7I5WgpJtN/norm.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/z7I5WgpJtN/norm.split.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/z7I5WgpJtN/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/z7I5WgpJtN/norm.split.2.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/z7I5WgpJtN/norm.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- --force /tmp/z7I5WgpJtN/norm.split.3.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- --force /tmp/z7I5WgpJtN/norm.split.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/z7I5WgpJtN/norm.split.4.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/z7I5WgpJtN/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- --keep-sum AD /tmp/z7I5WgpJtN/norm.split.4.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- --keep-sum AD /tmp/z7I5WgpJtN/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/z7I5WgpJtN/norm.split.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/z7I5WgpJtN/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/z7I5WgpJtN/norm.merge.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/z7I5WgpJtN/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/z7I5WgpJtN/norm.merge.2.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/z7I5WgpJtN/norm.merge.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/z7I5WgpJtN/norm.merge.3.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/z7I5WgpJtN/norm.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m+ -s /tmp/z7I5WgpJtN/norm.merge.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m+ -s /tmp/z7I5WgpJtN/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -Nc s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/z7I5WgpJtN/norm.setref.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -Nc s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/z7I5WgpJtN/norm.setref.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/z7I5WgpJtN/norm.telomere.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/z7I5WgpJtN/norm.telomere.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d snps /tmp/z7I5WgpJtN/norm.rmdup.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d snps /tmp/z7I5WgpJtN/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d indels /tmp/z7I5WgpJtN/norm.rmdup.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d indels /tmp/z7I5WgpJtN/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d both /tmp/z7I5WgpJtN/norm.rmdup.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d both /tmp/z7I5WgpJtN/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d all /tmp/z7I5WgpJtN/norm.rmdup.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d all /tmp/z7I5WgpJtN/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d none /tmp/z7I5WgpJtN/norm.rmdup.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d none /tmp/z7I5WgpJtN/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d exact /tmp/z7I5WgpJtN/norm.rmdup.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d exact /tmp/z7I5WgpJtN/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d none /tmp/z7I5WgpJtN/norm.rmdup.2.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d none /tmp/z7I5WgpJtN/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d exact /tmp/z7I5WgpJtN/norm.rmdup.2.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d exact /tmp/z7I5WgpJtN/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d indels /tmp/z7I5WgpJtN/norm.rmdup.2.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d indels /tmp/z7I5WgpJtN/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d any /tmp/z7I5WgpJtN/norm.rmdup.2.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d any /tmp/z7I5WgpJtN/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d both /tmp/z7I5WgpJtN/norm.rmdup.2.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d both /tmp/z7I5WgpJtN/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d snps /tmp/z7I5WgpJtN/norm.rmdup.2.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d snps /tmp/z7I5WgpJtN/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -c s -a -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.2.fa /tmp/z7I5WgpJtN/norm.2.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -c s -a -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.2.fa /tmp/z7I5WgpJtN/norm.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -c s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.iupac.fa /tmp/z7I5WgpJtN/norm.iupac.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -c s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.iupac.fa /tmp/z7I5WgpJtN/norm.iupac.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -c s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.3.fa /tmp/z7I5WgpJtN/norm.3.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -c s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.3.fa /tmp/z7I5WgpJtN/norm.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/z7I5WgpJtN/atomize.split.1.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/z7I5WgpJtN/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/z7I5WgpJtN/atomize.split.1.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/z7I5WgpJtN/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/z7I5WgpJtN/atomize.split.2.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/z7I5WgpJtN/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/z7I5WgpJtN/atomize.split.2.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/z7I5WgpJtN/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . /tmp/z7I5WgpJtN/atomize.split.3.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . /tmp/z7I5WgpJtN/atomize.split.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m +both /tmp/z7I5WgpJtN/norm.4.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m +both /tmp/z7I5WgpJtN/norm.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m +any /tmp/z7I5WgpJtN/norm.4.vcf.gz
.. ok
test_vcf_norm:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m +any /tmp/z7I5WgpJtN/norm.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/z7I5WgpJtN/view.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/z7I5WgpJtN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -f PASS -Xks NA00003 /tmp/z7I5WgpJtN/view.vcf.gz -r20,Y
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -f PASS -Xks NA00003 /tmp/z7I5WgpJtN/view.vcf.gz -r20,Y | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -xs NA00003 /tmp/z7I5WgpJtN/view.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -xs NA00003 /tmp/z7I5WgpJtN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/z7I5WgpJtN/view.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/z7I5WgpJtN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -p /tmp/z7I5WgpJtN/view.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -p /tmp/z7I5WgpJtN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -P /tmp/z7I5WgpJtN/view.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -P /tmp/z7I5WgpJtN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/z7I5WgpJtN/view.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/z7I5WgpJtN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -Hu /tmp/z7I5WgpJtN/view.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -GVsnps /tmp/z7I5WgpJtN/view.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -GVsnps /tmp/z7I5WgpJtN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/z7I5WgpJtN/view.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/z7I5WgpJtN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -s ^NA00003 /tmp/z7I5WgpJtN/view.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -s ^NA00003 /tmp/z7I5WgpJtN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version /tmp/z7I5WgpJtN/view.omitgenotypes.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -G /tmp/z7I5WgpJtN/view.omitgenotypes.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -G /tmp/z7I5WgpJtN/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -HG /tmp/z7I5WgpJtN/view.omitgenotypes.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -a /tmp/z7I5WgpJtN/many.alleles.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -a /tmp/z7I5WgpJtN/many.alleles.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -asA /tmp/z7I5WgpJtN/view.vectors.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -asA /tmp/z7I5WgpJtN/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -asB /tmp/z7I5WgpJtN/view.vectors.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -asB /tmp/z7I5WgpJtN/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -asA /tmp/z7I5WgpJtN/view.vectors.2.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -asA /tmp/z7I5WgpJtN/view.vectors.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'TXT0="text"' /tmp/z7I5WgpJtN/view.filter.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.chrs.tab /tmp/z7I5WgpJtN/view.chrs.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.chrs.tab /tmp/z7I5WgpJtN/view.chrs.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -i 'POS>=3062917' /tmp/z7I5WgpJtN/filter.2.vcf.gz 1:3062917-3157410
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -i 'POS>=3062917' /tmp/z7I5WgpJtN/filter.2.vcf.gz 1:3062917-3157410 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/z7I5WgpJtN/idx.1.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/z7I5WgpJtN/idx.2.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/idx.2.bed /tmp/z7I5WgpJtN/idx.2.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/idx.3.bed /tmp/z7I5WgpJtN/idx.3.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/idx.4.bed /tmp/z7I5WgpJtN/idx.4.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -Ht 2 /tmp/z7I5WgpJtN/view-t.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -Ht 3 /tmp/z7I5WgpJtN/view-t.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/z7I5WgpJtN/overlap.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/z7I5WgpJtN/overlap.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/z7I5WgpJtN/overlap.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/z7I5WgpJtN/overlap.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/z7I5WgpJtN/overlap.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/z7I5WgpJtN/overlap.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/z7I5WgpJtN/overlap.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/z7I5WgpJtN/overlap.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/z7I5WgpJtN/overlap.vcf.gz
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.1.vcf -H
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.1.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.2.vcf -H
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.2.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.3.vcf -H
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.4.vcf -H
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.4.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.5.vcf -H
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H
.. ok
test_vcf_64bit:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.5.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -C5:nonmajor /tmp/z7I5WgpJtN/view.minmaxac.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -c6:nonmajor /tmp/z7I5WgpJtN/view.minmaxac.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -q0.3:major /tmp/z7I5WgpJtN/view.minmaxac.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/z7I5WgpJtN/view.filter.annovar.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/z7I5WgpJtN/view.filter.annovar.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/z7I5WgpJtN/view.filter.annovar.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -a /tmp/z7I5WgpJtN/view-a.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.sites.txt /tmp/z7I5WgpJtN/view.sites.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.sites.txt /tmp/z7I5WgpJtN/view.sites.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.sites.txt.gz /tmp/z7I5WgpJtN/view.sites.vcf.gz
.. ok
test_vcf_view:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.sites.txt.gz /tmp/z7I5WgpJtN/view.sites.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_head:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf
.. ok
test_vcf_head:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf
.. ok
test_vcf_head:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf
.. ok
test_vcf_head:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 5 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf
.. ok
test_vcf_head:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 22 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf
.. ok
test_vcf_head:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 23 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf
.. ok
test_vcf_head:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -n 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf
.. ok
test_vcf_head:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -n 1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf
.. ok
test_vcf_head:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -n 5 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf
.. ok
test_vcf_head:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 5 -n 5 < /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mg0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mg0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.4.vcf
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.5.vcf
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.cals.1.vcf
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.cals.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.cals.2.vcf
.. ok
test_vcf_call_cAls:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/z7I5WgpJtN/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.cals.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -cv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -cv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.2.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf
.. ok
test_vcf_call:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.2.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'ALT="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'ALT="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.4.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.4.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="A"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="A"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="RR"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="RR"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="RA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="RA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="AR"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="AR"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="AA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="AA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="aA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="aA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="HET"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="HET"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%FR]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%FR]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%QUAL\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%QUAL\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.7.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.7.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.9.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.9.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_sort:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools sort -m 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok
test_vcf_sort:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools sort -Ob -m 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok
test_vcf_sort:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools sort -m 1000 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok
test_vcf_sort:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools sort -Ob -m 1000 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok
test_vcf_regions:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/regions.tab /tmp/z7I5WgpJtN/regions.vcf.gz
.. ok
test_vcf_regions:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/regions.tab
.. ok
test_vcf_regions:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/regions.tab /tmp/z7I5WgpJtN/regions.vcf.gz
.. ok
test_vcf_regions:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/z7I5WgpJtN/regions.tab.gz /tmp/z7I5WgpJtN/regions.vcf.gz
.. ok
test_vcf_regions:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/z7I5WgpJtN/regions.tab.gz
.. ok
test_vcf_regions:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/z7I5WgpJtN/regions.tab.gz /tmp/z7I5WgpJtN/regions.vcf.gz
.. ok
test_vcf_regions:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/z7I5WgpJtN/regions.bed /tmp/z7I5WgpJtN/regions.vcf.gz
.. ok
test_vcf_regions:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/z7I5WgpJtN/regions.bed
.. ok
test_vcf_regions:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/z7I5WgpJtN/regions.bed /tmp/z7I5WgpJtN/regions.vcf.gz
.. ok
test_vcf_regions:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/z7I5WgpJtN/regions.bed.gz /tmp/z7I5WgpJtN/regions.vcf.gz
.. ok
test_vcf_regions:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/z7I5WgpJtN/regions.bed.gz
.. ok
test_vcf_regions:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/z7I5WgpJtN/regions.bed.gz /tmp/z7I5WgpJtN/regions.vcf.gz
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/z7I5WgpJtN/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/z7I5WgpJtN/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -x FORMAT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -x FORMAT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots4.vcf.gz -c +INFO /tmp/z7I5WgpJtN/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots4.vcf.gz -c +INFO /tmp/z7I5WgpJtN/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots11.vcf.gz -c FMT /tmp/z7I5WgpJtN/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots11.vcf.gz -c FMT /tmp/z7I5WgpJtN/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c FMT/newGT:=GT /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots2.vcf.gz -c FMT/newGT:=GT /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots12.vcf.gz -c FMT/GT:=newGT /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots12.vcf.gz -c FMT/GT:=newGT /tmp/z7I5WgpJtN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -x FILTER /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -x FILTER /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/z7I5WgpJtN/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/z7I5WgpJtN/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/z7I5WgpJtN/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/z7I5WgpJtN/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate20.src.vcf.gz -c FMT/GT /tmp/z7I5WgpJtN/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate20.src.vcf.gz -c FMT/GT /tmp/z7I5WgpJtN/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate20.src.vcf.gz -c +FMT/GT /tmp/z7I5WgpJtN/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate20.src.vcf.gz -c +FMT/GT /tmp/z7I5WgpJtN/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate20.src.vcf.gz -c -FMT/GT /tmp/z7I5WgpJtN/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate20.src.vcf.gz -c -FMT/GT /tmp/z7I5WgpJtN/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-annots /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.txt /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob --rename-annots /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.txt /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/z7I5WgpJtN/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/z7I5WgpJtN/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate24.src.vcf.gz -c XX /tmp/z7I5WgpJtN/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate24.src.vcf.gz -c XX /tmp/z7I5WgpJtN/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate26.tab.gz -c CHROM,POS,~POS /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate26.tab.gz -c CHROM,POS,~POS /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots.id.vcf.gz -c ALT /tmp/z7I5WgpJtN/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots.id.vcf.gz -c ALT /tmp/z7I5WgpJtN/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/z7I5WgpJtN/annots.id.vcf.gz -c +ALT /tmp/z7I5WgpJtN/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/z7I5WgpJtN/annots.id.vcf.gz -c +ALT /tmp/z7I5WgpJtN/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/z7I5WgpJtN/checkploidy.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/z7I5WgpJtN/checkploidy.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/z7I5WgpJtN/checkploidy.2.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/z7I5WgpJtN/checkploidy.2.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/z7I5WgpJtN/checkploidy.2.vcf.gz -- -m | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/z7I5WgpJtN/checkploidy.2.bcf -- -m | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +missing2ref --no-version /tmp/z7I5WgpJtN/plugin1.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +missing2ref --no-version /tmp/z7I5WgpJtN/plugin1.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/plugin1.vcf.gz -- -t . -n 0 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/plugin1.bcf -- -t . -n 0 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.3.vcf.gz -- -t a -n pM | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.3.bcf -- -t a -n pM | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.3.vcf.gz -- -t a -n pm | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.3.bcf -- -t a -n pm | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.3.vcf.gz -- -t a -n c:1 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.3.bcf -- -t a -n c:1 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.3.vcf.gz -- -t a -n c:"1|1" | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.3.bcf -- -t a -n c:"1|1" | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.3.vcf.gz -- -t a -n c:"m|M" | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.3.bcf -- -t a -n c:"m|M" | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.3.vcf.gz -- -t a -n c:0/1/1 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.3.bcf -- -t a -n c:0/1/1 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.4.bcf -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/z7I5WgpJtN/setGT.4.bcf -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-AN-AC --no-version /tmp/z7I5WgpJtN/plugin1.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-AN-AC --no-version /tmp/z7I5WgpJtN/plugin1.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/z7I5WgpJtN/dosage.vcf.gz -- -t PL | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/z7I5WgpJtN/dosage.bcf -- -t PL | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/z7I5WgpJtN/dosage.vcf.gz -- -t GL | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/z7I5WgpJtN/dosage.bcf -- -t GL | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/z7I5WgpJtN/dosage.vcf.gz -- -t GT | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/z7I5WgpJtN/dosage.bcf -- -t GT | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixploidy --no-version /tmp/z7I5WgpJtN/fixploidy.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixploidy.ploidy | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixploidy --no-version /tmp/z7I5WgpJtN/fixploidy.bcf -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixploidy.ploidy | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +guess-ploidy /tmp/z7I5WgpJtN/view.PL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +guess-ploidy /tmp/z7I5WgpJtN/view.PL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +guess-ploidy /tmp/z7I5WgpJtN/view.GL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +guess-ploidy /tmp/z7I5WgpJtN/view.GL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/z7I5WgpJtN/view.GL.vcf.gz -- -r --gl-to-pl | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/z7I5WgpJtN/view.GL.bcf -- -r --gl-to-pl | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/z7I5WgpJtN/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/z7I5WgpJtN/view.GP.bcf -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +add-variantkey /tmp/z7I5WgpJtN/query.variantkey.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +add-variantkey /tmp/z7I5WgpJtN/query.variantkey.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +variantkey-hex /tmp/z7I5WgpJtN/query.variantkey.vcf.gz test/ | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +variantkey-hex /tmp/z7I5WgpJtN/query.variantkey.bcf test/ | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +allele-length /tmp/z7I5WgpJtN/query.nucleotide.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +allele-length /tmp/z7I5WgpJtN/query.nucleotide.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/view.vcf.gz -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/view.bcf -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/view.vcf.gz -- -t AC -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/view.bcf -- -t AC -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/view.vcf.gz -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/view.bcf -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/many-alts.vcf.gz -- -t AN,AC | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/many-alts.bcf -- -t AN,AC | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-hemi.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-hemi.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-hemi.vcf.gz -- -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-hemi.bcf -- -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-hwe.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-hwe.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-hwe.vcf.gz -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-hwe.bcf -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-AN0.vcf.gz -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-AN0.bcf -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-VAF.vcf.gz -- -t VAF,VAF1 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-VAF.bcf -- -t VAF,VAF1 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/fill-tags-AD.bcf -- -t 'FORMAT/DP:1=int(smpl_sum(FMT/AD))' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.vcf.gz | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.bcf | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.vcf.gz -- -H | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.bcf -- -H | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.vcf.gz -- -Hm | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.bcf -- -Hm | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.vcf.gz -- -Hmv | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.bcf -- -Hmv | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.vcf.gz -- -Hv | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.bcf -- -Hv | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.vcf.gz -- -m | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.bcf -- -m | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.vcf.gz -- -mv | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.bcf -- -mv | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.vcf.gz -- -v | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/z7I5WgpJtN/view.bcf -- -v | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-switch-rate /tmp/z7I5WgpJtN/trio.vcf.gz -- -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-switch-rate /tmp/z7I5WgpJtN/trio.bcf -- -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-stats /tmp/z7I5WgpJtN/trio-stats.vcf.gz -a 1 -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-stats /tmp/z7I5WgpJtN/trio-stats.bcf -a 1 -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-stats /tmp/z7I5WgpJtN/trio-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-stats /tmp/z7I5WgpJtN/trio-stats.bcf -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +smpl-stats /tmp/z7I5WgpJtN/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +smpl-stats /tmp/z7I5WgpJtN/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/z7I5WgpJtN/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/z7I5WgpJtN/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/z7I5WgpJtN/indel-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/z7I5WgpJtN/indel-stats.bcf -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/z7I5WgpJtN/indel-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/z7I5WgpJtN/indel-stats.bcf -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/z7I5WgpJtN/ad-bias.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/z7I5WgpJtN/ad-bias.bcf -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/z7I5WgpJtN/ad-bias.2.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/z7I5WgpJtN/ad-bias.2.bcf -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/z7I5WgpJtN/ad-bias.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/z7I5WgpJtN/ad-bias.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/z7I5WgpJtN/ad-bias.2.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/z7I5WgpJtN/ad-bias.2.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +af-dist /tmp/z7I5WgpJtN/af-dist.vcf.gz | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +af-dist /tmp/z7I5WgpJtN/af-dist.bcf | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/z7I5WgpJtN/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -i /tmp/z7I5WgpJtN/fixref.2b.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/z7I5WgpJtN/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -i /tmp/z7I5WgpJtN/fixref.2b.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/z7I5WgpJtN/fixref.3.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixref.3.fa -m top | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/z7I5WgpJtN/fixref.3.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixref.3.fa -m top | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/z7I5WgpJtN/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m ref-alt | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/z7I5WgpJtN/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m ref-alt | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/z7I5WgpJtN/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m flip | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/z7I5WgpJtN/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m flip | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/z7I5WgpJtN/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m flip-all | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/z7I5WgpJtN/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m flip-all | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/z7I5WgpJtN/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/z7I5WgpJtN/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/z7I5WgpJtN/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.fa -c REF -N | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/z7I5WgpJtN/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.fa -c REF -N | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/z7I5WgpJtN/ref.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -c REF | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/z7I5WgpJtN/ref.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -c REF | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/z7I5WgpJtN/view.vcf.gz -- -s NA00001 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/z7I5WgpJtN/view.bcf -- -s NA00001 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/z7I5WgpJtN/view.vcf.gz -- -s NA00001,NA00002 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/z7I5WgpJtN/view.bcf -- -s NA00001,NA00002 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/z7I5WgpJtN/view.vcf.gz -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/z7I5WgpJtN/view.bcf -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/z7I5WgpJtN/mendelian.vcf.gz -t mom1,dad1,child1 -md | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/z7I5WgpJtN/mendelian.bcf -t mom1,dad1,child1 -md | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/z7I5WgpJtN/mendelian.vcf.gz -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/z7I5WgpJtN/mendelian.bcf -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/z7I5WgpJtN/mendelian.vcf.gz -t mom1,dad1,child1 -mx | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/z7I5WgpJtN/mendelian.bcf -t mom1,dad1,child1 -mx | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/z7I5WgpJtN/mendelian.vcf.gz -t mom1,dad1,child1 -ma | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/z7I5WgpJtN/mendelian.bcf -t mom1,dad1,child1 -ma | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/z7I5WgpJtN/mendelian.vcf.gz -t mom1,dad1,child1 -mu | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/z7I5WgpJtN/mendelian.bcf -t mom1,dad1,child1 -mu | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/z7I5WgpJtN/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/z7I5WgpJtN/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/z7I5WgpJtN/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/contrast1.txt | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/z7I5WgpJtN/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/contrast1.txt | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/z7I5WgpJtN/contrast.vcf.gz -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/z7I5WgpJtN/contrast.bcf -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/z7I5WgpJtN/contrast.1.vcf.gz -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/z7I5WgpJtN/contrast.1.bcf -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/z7I5WgpJtN/contrast.1.vcf.gz -a NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/z7I5WgpJtN/contrast.1.bcf -a NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.1.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.1.bcf -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.2.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.2.bcf -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.4.bcf -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.8.vcf.gz -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.8.bcf -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.9.vcf.gz -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.9.bcf -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.9.vcf.gz -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.9.bcf -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.10.vcf.gz -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/z7I5WgpJtN/trio-dnm/trio-dnm.10.bcf -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/z7I5WgpJtN/gvcfz.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/z7I5WgpJtN/gvcfz.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/z7I5WgpJtN/gvcfz.vcf.gz -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/z7I5WgpJtN/gvcfz.bcf -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/z7I5WgpJtN/gvcfz.2.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/z7I5WgpJtN/gvcfz.2.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools +remove-overlaps /tmp/z7I5WgpJtN/remove-overlaps.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +remove-overlaps /tmp/z7I5WgpJtN/remove-overlaps.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +remove-overlaps /tmp/z7I5WgpJtN/remove-overlaps.vcf.gz -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +remove-overlaps /tmp/z7I5WgpJtN/remove-overlaps.bcf -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.vcf.gz -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.bcf -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.vcf.gz -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.bcf -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.vcf.gz -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.bcf -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.2.vcf.gz -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.2.bcf -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.2.vcf.gz -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.2.bcf -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.3.vcf.gz -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.3.bcf -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.vcf.gz -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.bcf -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.vcf.gz -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.bcf -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.5.vcf.gz -s :synonymous -c Consequence | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.5.bcf -s :synonymous -c Consequence | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.5.vcf.gz -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.5.bcf -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.6.vcf.gz -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.6.bcf -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.6.vcf.gz -c - | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.6.bcf -c - | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.6.vcf.gz -c - -s worst | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/split-vep.6.bcf -c - -s worst | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/z7I5WgpJtN/prune.1.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/z7I5WgpJtN/prune.1.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/z7I5WgpJtN/prune.2.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/z7I5WgpJtN/prune.2.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/z7I5WgpJtN/prune.1.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/z7I5WgpJtN/prune.1.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/z7I5WgpJtN/prune.1.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/z7I5WgpJtN/prune.1.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/z7I5WgpJtN/prune.1.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/z7I5WgpJtN/prune.1.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/z7I5WgpJtN/prune.1.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/z7I5WgpJtN/prune.1.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N 1st /tmp/z7I5WgpJtN/prune.1.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N 1st /tmp/z7I5WgpJtN/prune.1.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/z7I5WgpJtN/prune.1.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/z7I5WgpJtN/prune.1.bcf | grep -v ^##bcftools_
.. ok
test_plugin_split:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/z7I5WgpJtN/split.1.1 && cd /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done
.. ok
test_plugin_split:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/z7I5WgpJtN/split.1.2 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.2.txt && cd /tmp/z7I5WgpJtN/split.1.2 && for f in A.vcf B.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done
.. ok
test_plugin_split:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/z7I5WgpJtN/split.1.3 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.3.txt && cd /tmp/z7I5WgpJtN/split.1.3 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done
.. ok
test_plugin_split:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/z7I5WgpJtN/split.1.4 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.3.txt -i 'GT[0]="alt"' && cd /tmp/z7I5WgpJtN/split.1.4 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done
.. ok
test_plugin_split:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/z7I5WgpJtN/split.1.5 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.3.txt -i 'GT="alt"' && cd /tmp/z7I5WgpJtN/split.1.5 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done
.. ok
test_plugin_split:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/z7I5WgpJtN/split.1.6 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.4.txt -i 'GT="alt"' && cd /tmp/z7I5WgpJtN/split.1.6 && for f in file1.vcf file2.vcf file3.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done
.. ok
test_plugin_split:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/z7I5WgpJtN/split.1.7 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.grp.1.1.txt && cd /tmp/z7I5WgpJtN/split.1.7 && for f in A.vcf A1.vcf A2.vcf B.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done
.. ok
test_plugin_split:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.2.vcf -o /tmp/z7I5WgpJtN/split.2.1 && cd /tmp/z7I5WgpJtN/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-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done
.. ok
test_plugin_scatter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/z7I5WgpJtN/scatter.1.1 -n 3 && cd /tmp/z7I5WgpJtN/scatter.1.1 && cat 0.vcf 1.vcf 2.vcf | grep -v ^##
.. ok
test_plugin_scatter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/z7I5WgpJtN/scatter.1.2 -s 21,22 && cd /tmp/z7I5WgpJtN/scatter.1.2 && cat 21.vcf 22.vcf | grep -v ^##
.. ok
test_plugin_scatter:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/z7I5WgpJtN/scatter.1.3 -s 21,22 -x X && cd /tmp/z7I5WgpJtN/scatter.1.3 && cat 21.vcf 22.vcf X.vcf | grep -v ^##
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version /tmp/z7I5WgpJtN/concat.1.a.vcf.gz /tmp/z7I5WgpJtN/concat.1.b.vcf.gz
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob /tmp/z7I5WgpJtN/concat.1.a.vcf.gz /tmp/z7I5WgpJtN/concat.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version /tmp/z7I5WgpJtN/concat.1.a.bcf /tmp/z7I5WgpJtN/concat.1.b.bcf
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob /tmp/z7I5WgpJtN/concat.1.a.bcf /tmp/z7I5WgpJtN/concat.1.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -a /tmp/z7I5WgpJtN/concat.2.a.vcf.gz /tmp/z7I5WgpJtN/concat.2.b.vcf.gz
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -a /tmp/z7I5WgpJtN/concat.2.a.vcf.gz /tmp/z7I5WgpJtN/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -a /tmp/z7I5WgpJtN/concat.2.a.bcf /tmp/z7I5WgpJtN/concat.2.b.bcf
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -a /tmp/z7I5WgpJtN/concat.2.a.bcf /tmp/z7I5WgpJtN/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -aD /tmp/z7I5WgpJtN/concat.2.a.vcf.gz /tmp/z7I5WgpJtN/concat.2.b.vcf.gz
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -aD /tmp/z7I5WgpJtN/concat.2.a.vcf.gz /tmp/z7I5WgpJtN/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -aD /tmp/z7I5WgpJtN/concat.2.a.bcf /tmp/z7I5WgpJtN/concat.2.b.bcf
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -aD /tmp/z7I5WgpJtN/concat.2.a.bcf /tmp/z7I5WgpJtN/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/z7I5WgpJtN/concat.3.a.vcf.gz /tmp/z7I5WgpJtN/concat.3.b.vcf.gz /tmp/z7I5WgpJtN/concat.3.0.vcf.gz /tmp/z7I5WgpJtN/concat.3.c.vcf.gz /tmp/z7I5WgpJtN/concat.3.d.vcf.gz /tmp/z7I5WgpJtN/concat.3.e.vcf.gz /tmp/z7I5WgpJtN/concat.3.f.vcf.gz
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/z7I5WgpJtN/concat.3.a.vcf.gz /tmp/z7I5WgpJtN/concat.3.b.vcf.gz /tmp/z7I5WgpJtN/concat.3.0.vcf.gz /tmp/z7I5WgpJtN/concat.3.c.vcf.gz /tmp/z7I5WgpJtN/concat.3.d.vcf.gz /tmp/z7I5WgpJtN/concat.3.e.vcf.gz /tmp/z7I5WgpJtN/concat.3.f.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/z7I5WgpJtN/concat.3.a.bcf /tmp/z7I5WgpJtN/concat.3.b.bcf /tmp/z7I5WgpJtN/concat.3.0.bcf /tmp/z7I5WgpJtN/concat.3.c.bcf /tmp/z7I5WgpJtN/concat.3.d.bcf /tmp/z7I5WgpJtN/concat.3.e.bcf /tmp/z7I5WgpJtN/concat.3.f.bcf
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/z7I5WgpJtN/concat.3.a.bcf /tmp/z7I5WgpJtN/concat.3.b.bcf /tmp/z7I5WgpJtN/concat.3.0.bcf /tmp/z7I5WgpJtN/concat.3.c.bcf /tmp/z7I5WgpJtN/concat.3.d.bcf /tmp/z7I5WgpJtN/concat.3.e.bcf /tmp/z7I5WgpJtN/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
Random seed for test_naive_concat: 118442687
.. ok
test_naive_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --naive-force /tmp/z7I5WgpJtN/naive_concat.0.bcf /tmp/z7I5WgpJtN/naive_concat.1.bcf /tmp/z7I5WgpJtN/naive_concat.2.bcf /tmp/z7I5WgpJtN/naive_concat.3.bcf /tmp/z7I5WgpJtN/naive_concat.4.bcf /tmp/z7I5WgpJtN/naive_concat.5.bcf /tmp/z7I5WgpJtN/naive_concat.6.bcf /tmp/z7I5WgpJtN/naive_concat.7.bcf /tmp/z7I5WgpJtN/naive_concat.8.bcf /tmp/z7I5WgpJtN/naive_concat.9.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H
.. ok
test_naive_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --naive /tmp/z7I5WgpJtN/naive_concat.0.vcf.gz /tmp/z7I5WgpJtN/naive_concat.1.vcf.gz /tmp/z7I5WgpJtN/naive_concat.2.vcf.gz /tmp/z7I5WgpJtN/naive_concat.3.vcf.gz /tmp/z7I5WgpJtN/naive_concat.4.vcf.gz /tmp/z7I5WgpJtN/naive_concat.5.vcf.gz /tmp/z7I5WgpJtN/naive_concat.6.vcf.gz /tmp/z7I5WgpJtN/naive_concat.7.vcf.gz /tmp/z7I5WgpJtN/naive_concat.8.vcf.gz /tmp/z7I5WgpJtN/naive_concat.9.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l /tmp/z7I5WgpJtN/concat.4.a.vcf.gz /tmp/z7I5WgpJtN/concat.4.b.vcf.gz
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l /tmp/z7I5WgpJtN/concat.4.a.vcf.gz /tmp/z7I5WgpJtN/concat.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l /tmp/z7I5WgpJtN/concat.4.a.bcf /tmp/z7I5WgpJtN/concat.4.b.bcf
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l /tmp/z7I5WgpJtN/concat.4.a.bcf /tmp/z7I5WgpJtN/concat.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/z7I5WgpJtN/concat.5.a.vcf.gz /tmp/z7I5WgpJtN/concat.5.b.vcf.gz /tmp/z7I5WgpJtN/concat.5.c.vcf.gz
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/z7I5WgpJtN/concat.5.a.vcf.gz /tmp/z7I5WgpJtN/concat.5.b.vcf.gz /tmp/z7I5WgpJtN/concat.5.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/z7I5WgpJtN/concat.5.a.bcf /tmp/z7I5WgpJtN/concat.5.b.bcf /tmp/z7I5WgpJtN/concat.5.c.bcf
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/z7I5WgpJtN/concat.5.a.bcf /tmp/z7I5WgpJtN/concat.5.b.bcf /tmp/z7I5WgpJtN/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-force /tmp/z7I5WgpJtN/concat.5.a.bcf /tmp/z7I5WgpJtN/concat.5.b.bcf /tmp/z7I5WgpJtN/concat.5.c.bcf
.. ok
test_vcf_concat:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-force /tmp/z7I5WgpJtN/concat.5.a.bcf /tmp/z7I5WgpJtN/concat.5.b.bcf /tmp/z7I5WgpJtN/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr /tmp/z7I5WgpJtN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /tmp/z7I5WgpJtN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr /tmp/z7I5WgpJtN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /tmp/z7I5WgpJtN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples /tmp/z7I5WgpJtN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /tmp/z7I5WgpJtN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples /tmp/z7I5WgpJtN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /tmp/z7I5WgpJtN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 /tmp/z7I5WgpJtN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /tmp/z7I5WgpJtN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 /tmp/z7I5WgpJtN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /tmp/z7I5WgpJtN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 /tmp/z7I5WgpJtN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /tmp/z7I5WgpJtN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 /tmp/z7I5WgpJtN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /tmp/z7I5WgpJtN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 /tmp/z7I5WgpJtN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /tmp/z7I5WgpJtN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 /tmp/z7I5WgpJtN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /tmp/z7I5WgpJtN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/empty.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/empty.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr /tmp/z7I5WgpJtN/empty.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /tmp/z7I5WgpJtN/empty.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr /tmp/z7I5WgpJtN/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /tmp/z7I5WgpJtN/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /tmp/z7I5WgpJtN/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /tmp/z7I5WgpJtN/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /tmp/z7I5WgpJtN/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_vcf_reheader:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /tmp/z7I5WgpJtN/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version
.. ok
test_rename_chrs:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/z7I5WgpJtN/rename.map -Ov /tmp/z7I5WgpJtN/annotate.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n'
.. ok
test_rename_chrs:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/z7I5WgpJtN/rename.map -Ob /tmp/z7I5WgpJtN/annotate.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n'
.. ok
test_rename_chrs:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/z7I5WgpJtN/rename.map -Ov /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n'
.. ok
test_rename_chrs:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/z7I5WgpJtN/rename.map -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n'
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. /tmp/z7I5WgpJtN/convert.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,.
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids /tmp/z7I5WgpJtN/convert.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids --3N6 /tmp/z7I5WgpJtN/convert.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids --3N6
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- /tmp/z7I5WgpJtN/convert.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,-
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --tag PL /tmp/z7I5WgpJtN/convert.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --tag PL
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --tag PL /tmp/z7I5WgpJtN/convert.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --tag PL
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids /tmp/z7I5WgpJtN/check.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --vcf-ids /tmp/z7I5WgpJtN/check.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --vcf-ids
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --3N6 /tmp/z7I5WgpJtN/check.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --3N6
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --3N6 /tmp/z7I5WgpJtN/check.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --3N6
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --3N6 --vcf-ids /tmp/z7I5WgpJtN/check.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --3N6 --vcf-ids
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --3N6 --vcf-ids /tmp/z7I5WgpJtN/check.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --3N6 --vcf-ids
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h -,.,. /tmp/z7I5WgpJtN/convert.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h -,.,.
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,-,. /tmp/z7I5WgpJtN/convert.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,-,.
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,-,. --vcf-ids /tmp/z7I5WgpJtN/convert.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,-,. --vcf-ids
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,.,- /tmp/z7I5WgpJtN/convert.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,.,-
.. ok
test_vcf_convert_hls2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -H /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.samples | grep -v ^##
.. ok
test_vcf_convert_hls2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -H /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --haplegendsample -,.,. /tmp/z7I5WgpJtN/convert.hap-missing.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.hap-missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --haplegendsample -,.,.
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample -,. /tmp/z7I5WgpJtN/convert.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample -,.
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample -,. --vcf-ids /tmp/z7I5WgpJtN/convert.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample -,. --vcf-ids
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample .,- /tmp/z7I5WgpJtN/convert.vcf.gz
.. ok
test_vcf_convert:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample .,-
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.samples | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.samples | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##
.. ok
test_vcf_convert_gvcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/z7I5WgpJtN/convert.gvcf.vcf.gz
.. ok
test_vcf_convert_gvcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/z7I5WgpJtN/convert.gvcf.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa | grep -v ^##bcftools
.. ok
test_vcf_convert_tsv2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.23andme
.. ok
test_vcf_convert_tsv2vcf:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.23andme | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab
.. ok
test_vcf_consensus_chain:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab -c /tmp/z7I5WgpJtN/consensus.1.chain.new >/dev/null; cat /tmp/z7I5WgpJtN/consensus.1.chain.new
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab
.. ok
test_vcf_consensus_chain:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab -c /tmp/z7I5WgpJtN/consensus.2.chain.new >/dev/null; cat /tmp/z7I5WgpJtN/consensus.2.chain.new
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab --mask-with X -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab --mask-with lc
.. ok
test_vcf_consensus_chain:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab -c /tmp/z7I5WgpJtN/consensus.3.chain.new >/dev/null; cat /tmp/z7I5WgpJtN/consensus.3.chain.new
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H 1
.. ok
test_vcf_consensus_chain:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H 1 -c /tmp/z7I5WgpJtN/consensus.4.chain.new >/dev/null; cat /tmp/z7I5WgpJtN/consensus.4.chain.new
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -H 1
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -H 2
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/empty.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -H 2 -M "?"
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -H 2 -M "?" -p xx_
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus4.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus5.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus5.fa --haplotype LA
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus6.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus6.fa
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus7.fa -H 2
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus7.fa -H 2pIu
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus7.fa -H 1
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus7.fa -H 1pIu
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a .
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . -i 'type="snp" || type="ref"'
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . -i 'ALT!="<DEL>"'
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . -e 'MinDP>15'
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . -e 'MinDP<15'
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.9.1.fa -H A
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.9.2.fa -H A
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.9.1.fa -H A
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.9.2.fa -H A
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.11.fa -s smpl
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.11.fa -s smpl -a N
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.12.fa
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.13.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.13.fa
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.14.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.14.fa
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.12.fa --mark-del - --mark-ins uc --mark-snv uc
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.15.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -I
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H I
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.17.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -M N -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.17.bed
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.18.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.18.fa
.. ok
test_vcf_consensus:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/z7I5WgpJtN/consensus.19.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.19.fa
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -b /tmp/z7I5WgpJtN/mpileup.bam.list --no-version | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob -b /tmp/z7I5WgpJtN/mpileup.bam.urllist | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -b /tmp/z7I5WgpJtN/mpileup.cram.list --no-version | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob -b /tmp/z7I5WgpJtN/mpileup.cram.urllist | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_csq:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.gff3 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.chr.gff3 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.2.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok
test_csq:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.2.gff --ncsq 64 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok
test_csq_real:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000624631/ENST00000624631.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000624631/ENST00000624631.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000624631/ambiguous.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000593942/ENST00000593942.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000593942/ENST00000593942.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000593942/last-codon-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000580206 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000557788/ENST00000557788.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000557788/ENST00000557788.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000557788/long-overlap-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000545279/ENST00000545279.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000545279/ENST00000545279.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000545279/splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000528237/ENST00000528237.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000528237/ENST00000528237.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520868/ENST00000520868.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520868/ENST00000520868.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520868/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000519442/ENST00000519442.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000519442/ENST00000519442.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000519442/synon-splice-region-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414/ENST00000518414.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414/ENST00000518414.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000448695/ENST00000448695.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000448695/ENST00000448695.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000436063/ENST00000436063.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000436063/ENST00000436063.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000436063/insert-before-utr.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000422159 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q
.. ok
test_csq_real:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/start-stop-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/segfault.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420190/ENST00000420190.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420190/ENST00000420190.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420190/abort-in-csq-push.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
.. ok
test_csq_real:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000413103/ENST00000413103.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000413103/ENST00000413103.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000413103/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009/ENST00000410009.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009/ENST00000410009.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009/frameshift.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000409523/ENST00000409523.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000409523/ENST00000409523.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000409523/long-overlapping-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000400151/ENST00000400151.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000400151/ENST00000400151.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000400151/long-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000390520/ENST00000390520.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000390520/ENST00000390520.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000390520/deletion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000382647/ENST00000382647.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000382647/ENST00000382647.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000381157/ENST00000381157.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000381157/ENST00000381157.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000381157/haploid-diploid.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
.. ok
test_csq_real:
cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000379416 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000375992/ENST00000375992.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000375992/ENST00000375992.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801/ENST00000368801.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801/ENST00000368801.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801/compound-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801.2/ENST00000368801.2.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801.2/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000357367/ENST00000357367.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000357367/ENST00000357367.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000357367/stop-retained.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249.2/ENST00000318249.2.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000301246/ENST00000301246.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000301246/ENST00000301246.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000301246/15bp-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000285021/ENST00000285021.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000285021/ENST00000285021.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000271583/ENST00000271583.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000271583/ENST00000271583.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000271583/splice-acceptor.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000269081/ENST00000269081.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000269081/ENST00000269081.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000263103-INS/insertions.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000256452/ENST00000256452.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000256452/ENST00000256452.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000256452/intron.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000230048/ENST00000230048.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000230048/ENST00000230048.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000230048/start-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000227471/ENST00000227471.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000227471/ENST00000227471.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/start-lost-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000000000 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q
.. ok
test_csq_real:
cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSMUST00000133836 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSG00000173376/ENSG00000173376.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSG00000173376/ENSG00000173376.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSG00000173376/synon.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0003/EDUMMY0003.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0003/EDUMMY0003.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0003/long-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0002/EDUMMY0002.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0002/EDUMMY0002.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0002/boundaries.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^#
.. ok
test_roh:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.tab.gz| grep -v ^#
.. ok
test_roh:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.tab.gz --ignore-homref| grep -v ^#
.. ok
test_roh:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^#
.. ok
test_roh:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/z7I5WgpJtN/gtcheck.1.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,GT /tmp/z7I5WgpJtN/gtcheck.1.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,PL /tmp/z7I5WgpJtN/gtcheck.1.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,GT /tmp/z7I5WgpJtN/gtcheck.1.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,PL /tmp/z7I5WgpJtN/gtcheck.1.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -p s1,s1 /tmp/z7I5WgpJtN/gtcheck.1.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/z7I5WgpJtN/gtcheck.2.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/z7I5WgpJtN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/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/z7I5WgpJtN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gtcheck.3.pairs /tmp/z7I5WgpJtN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL /tmp/z7I5WgpJtN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 --n-matches 4 /tmp/z7I5WgpJtN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/z7I5WgpJtN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/z7I5WgpJtN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/z7I5WgpJtN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/z7I5WgpJtN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/z7I5WgpJtN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -p B,C,B,D /tmp/z7I5WgpJtN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,GT -H /tmp/z7I5WgpJtN/gtcheck.1.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,PL -H /tmp/z7I5WgpJtN/gtcheck.1.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,GT -H /tmp/z7I5WgpJtN/gtcheck.1.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,PL -H /tmp/z7I5WgpJtN/gtcheck.1.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/z7I5WgpJtN/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/z7I5WgpJtN/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -u GT -e 30 /tmp/z7I5WgpJtN/gtcheck.1.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/z7I5WgpJtN/gtcheck.1.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -u GT -e 300 /tmp/z7I5WgpJtN/gtcheck.1.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -u PL -e 30 /tmp/z7I5WgpJtN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck /tmp/z7I5WgpJtN/gtcheck.ntop.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck --n-matches 2 /tmp/z7I5WgpJtN/gtcheck.ntop.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck /tmp/z7I5WgpJtN/gtcheck.5.vcf.gz -g /tmp/z7I5WgpJtN/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time
.. ok
Number of tests:
total .. 1725
passed .. 1725
failed .. 0
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: bcftools-1.15.1-10.fc42.aarch64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.0Y6NPf
+ umask 022
+ cd /builddir/build/BUILD/bcftools-1.15.1-build
+ cd bcftools-1.15.1
+ DOCDIR=/builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/doc/bcftools
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/doc/bcftools
+ cp -pr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/AUTHORS /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/doc/bcftools
+ cp -pr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/NEWS /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/doc/bcftools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.gsODnv
+ umask 022
+ cd /builddir/build/BUILD/bcftools-1.15.1-build
+ cd bcftools-1.15.1
+ LICENSEDIR=/builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/licenses/bcftools
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/licenses/bcftools
+ cp -pr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/LICENSE /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/licenses/bcftools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: bcftools = 1.15.1-10.fc42 bcftools(aarch-64) = 1.15.1-10.fc42
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 ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgsl.so.27()(64bit) libgslcblas.so.0()(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libperl.so.5.40()(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Conflicts: samtools < 1.0
Processing files: bcftools-debugsource-1.15.1-10.fc42.aarch64
Provides: bcftools-debugsource = 1.15.1-10.fc42 bcftools-debugsource(aarch-64) = 1.15.1-10.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: bcftools-debuginfo-1.15.1-10.fc42.aarch64
Provides: bcftools-debuginfo = 1.15.1-10.fc42 bcftools-debuginfo(aarch-64) = 1.15.1-10.fc42 debuginfo(build-id) = 02586977b241e780b7712a2746b03fa64e5985ea debuginfo(build-id) = 0c8887db35c89d37cdfeca91b6421162be385803 debuginfo(build-id) = 0d8399c8706d336faa203b8857bd6d4e40ad4377 debuginfo(build-id) = 132db2e9e18b22bb45e829d46bce5cc6ccc31455 debuginfo(build-id) = 14c929d4d9a96f0c076d9ba8459d0239529d8457 debuginfo(build-id) = 171cbce7c5bc88334cad305015b031d915bbbeb9 debuginfo(build-id) = 192c258531609320b8f0fcc81dba5aaea554d5a3 debuginfo(build-id) = 1e1ebc8eca2c3dd672f899594a80f440777d64f0 debuginfo(build-id) = 2496fd6cfd9390ec58424ddb19dc4fee28595544 debuginfo(build-id) = 27e6930e1d9bba6d167daf3f6db83b09737f9b44 debuginfo(build-id) = 2d9d74dabe2dee9396c3e5dcf2b741aea55a8133 debuginfo(build-id) = 2e3c827665720037d8e0b3d19b3ff08a51835703 debuginfo(build-id) = 2e776e56a23ab881a6518f5930347e369d6efdf4 debuginfo(build-id) = 3ec14ed3ee868f47f9f4c0b7b8307f8eabb3e7f6 debuginfo(build-id) = 4321dd1cd094db5002707e30c4740454d94fb2d2 debuginfo(build-id) = 5616155c234819c804b824f65bd83ea413ec46c1 debuginfo(build-id) = 5a22dfa1fc6e5661bb677b9908d7c55f69da6b04 debuginfo(build-id) = 5bea4260ea3397cd109d78c8825e16b1e501270a debuginfo(build-id) = 5e6f84a7b3dbba56e9fd3767d621103f5b5f724c debuginfo(build-id) = 61e03cc21aeb72eb84606a680aace4eedee6ae6c debuginfo(build-id) = 7be4eed5e9b0ac94f57c9bd00b3764b78bd8abdf debuginfo(build-id) = 83945d4081782d55e3794d7ca6774ca5c6578415 debuginfo(build-id) = 852783f09e58b956983a167a5c71a1380b674c1d debuginfo(build-id) = 9078b30a7cfe3eebe5305bc4012277dc5ee96989 debuginfo(build-id) = 96b98e90521990228176556f42cf3d0b5587cb84 debuginfo(build-id) = 9f98198c6b6ae79fa856846e3af6efa2befc1ae3 debuginfo(build-id) = bf93b5102c597f992c9f1ec523cf8056f1b460fc debuginfo(build-id) = ca93385f65d71989e817f4c072894acc2b43bf08 debuginfo(build-id) = cd85941cf89be37a9695ba8fed36289f1b2dd561 debuginfo(build-id) = cfb1b88da130df15742367ca83267b9144479454 debuginfo(build-id) = d627922ea014c8007a73a6322e307200a003de6f debuginfo(build-id) = eaeeb1fd7fd345bc2bc02907a74a8bd60e62d1bc debuginfo(build-id) = ed93e05b8d61678776ddf31036ba0bf0d1cc8509 debuginfo(build-id) = f1dbc44c63bdc3fd3b30ff9069e0b152559c8d60 debuginfo(build-id) = f52e09eba6fc1f2b18f9791a96c6ad73c383d5e2 debuginfo(build-id) = f89bbcbc90335b191b6ee5a73ce5bd53af7ffe14 debuginfo(build-id) = f97a6c2c5475c010278f7bc215abe335ad15143b debuginfo(build-id) = fae3d357f784f49b80ad8bee678673ef6df5c20d debuginfo(build-id) = fbf50d722d72a26679abe83719274819373cb441
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: bcftools-debugsource(aarch-64) = 1.15.1-10.fc42
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT
Wrote: /builddir/build/RPMS/bcftools-1.15.1-10.fc42.aarch64.rpm
Wrote: /builddir/build/RPMS/bcftools-debugsource-1.15.1-10.fc42.aarch64.rpm
Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.15.1-10.fc42.aarch64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.RyXyzr
+ umask 022
+ cd /builddir/build/BUILD/bcftools-1.15.1-build
+ test -d /builddir/build/BUILD/bcftools-1.15.1-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/bcftools-1.15.1-build
+ rm -rf /builddir/build/BUILD/bcftools-1.15.1-build
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild bcftools-1.15.1-10.fc42.src.rpm
Finish: build phase for bcftools-1.15.1-10.fc42.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-aarch64-1727274377.320064/root/var/log/dnf5.log
INFO: Done(/var/lib/copr-rpmbuild/results/bcftools-1.15.1-10.fc42.src.rpm) Config(child) 1 minutes 12 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-debuginfo",
"epoch": null,
"version": "1.15.1",
"release": "10.fc42",
"arch": "aarch64"
},
{
"name": "bcftools",
"epoch": null,
"version": "1.15.1",
"release": "10.fc42",
"arch": "src"
},
{
"name": "bcftools-debugsource",
"epoch": null,
"version": "1.15.1",
"release": "10.fc42",
"arch": "aarch64"
},
{
"name": "bcftools",
"epoch": null,
"version": "1.15.1",
"release": "10.fc42",
"arch": "aarch64"
}
]
}
RPMResults finished