Warning: Permanently added '44.210.95.121' (ED25519) to the list of known hosts. Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5168090 --chroot fedora-rawhide-x86_64 --detached Version: 0.62 PID: 11367 Logging PID: 11368 Task: {'appstream': False, 'background': True, 'build_id': 5168090, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '247dd68fc6e270b5ceaa21ab6ec828b82f7f3dce', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/bcftools', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'bcftools', 'package_version': '1.15.1-2', 'project_dirname': 'gcc-13-test', 'project_name': 'gcc-13-test', 'project_owner': 'jakub', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jakub/gcc-13-test/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository'}, {'baseurl': 'https://jakub.fedorapeople.org/fedora-gcc13-$arch/', 'id': 'https_jakub_fedorapeople_org_fedora_gcc13_arch', 'name': 'Additional repo https_jakub_fedorapeople_org_fedora_gcc13_arch'}], 'sandbox': 'jakub/gcc-13-test--jakub', 'source_json': {}, 'source_type': None, 'submitter': 'jakub', 'tags': [], 'task_id': '5168090-fedora-rawhide-x86_64', 'timeout': 115200, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/bcftools /var/lib/copr-rpmbuild/workspace/workdir-xqei4s3q/bcftools --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/bcftools', '/var/lib/copr-rpmbuild/workspace/workdir-xqei4s3q/bcftools', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-xqei4s3q/bcftools'... Running: git checkout 247dd68fc6e270b5ceaa21ab6ec828b82f7f3dce cmd: ['git', 'checkout', '247dd68fc6e270b5ceaa21ab6ec828b82f7f3dce'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-xqei4s3q/bcftools rc: 0 stdout: stderr: Note: switching to '247dd68fc6e270b5ceaa21ab6ec828b82f7f3dce'. 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 Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 247dd68 automatic import of bcftools Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-xqei4s3q/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 /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated INFO: Calling: curl -H Pragma: -o bcftools-1.15.1.tar.bz2 --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jakub/gcc-13-test/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 100 6755k 100 6755k 0 0 33.9M 0 --:--:-- --:--:-- --:--:-- 34.0M INFO: Reading stdout from command: md5sum bcftools-1.15.1.tar.bz2 Running (timeout=115200): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-xqei4s3q/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-xqei4s3q/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1671795578.114598 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)... 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-xqei4s3q/bcftools/bcftools.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1671795578.114598/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: enabled HW Info plugin Mock Version: 3.5 INFO: Mock Version: 3.5 Start(bootstrap): dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 43 MB/s | 3.7 MB 00:00 Additional repo https_jakub_fedorapeople_org_fe 525 kB/s | 92 kB 00:00 fedora 27 MB/s | 65 MB 00:02 Dependencies resolved. ========================================================================================================================= Package Arch Version Repository Size ========================================================================================================================= Installing: dnf noarch 4.14.0-1.fc38 fedora 480 k dnf-plugins-core noarch 4.3.1-1.fc38 fedora 34 k Installing dependencies: alternatives x86_64 1.21-1.fc38 fedora 38 k audit-libs x86_64 3.0.9-1.fc38 copr_base 117 k basesystem noarch 11-14.fc37 fedora 7.0 k bash x86_64 5.2.9-3.fc38 copr_base 1.8 M bzip2-libs x86_64 1.0.8-12.fc37 fedora 41 k ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k coreutils x86_64 9.1-8.fc38 fedora 1.1 M coreutils-common x86_64 9.1-8.fc38 fedora 2.0 M crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k curl x86_64 7.87.0-1.fc38 fedora 344 k cyrus-sasl-lib x86_64 2.1.28-8.fc38 fedora 792 k dbus-libs x86_64 1:1.14.4-1.fc38 fedora 156 k dnf-data noarch 4.14.0-1.fc38 fedora 43 k elfutils-default-yama-scope noarch 0.188-3.fc38 fedora 15 k elfutils-libelf x86_64 0.188-3.fc38 fedora 196 k elfutils-libs x86_64 0.188-3.fc38 fedora 257 k expat x86_64 2.5.0-1.fc38 fedora 110 k fedora-gpg-keys noarch 38-0.3 fedora 125 k fedora-release noarch 38-0.6 fedora 11 k fedora-release-common noarch 38-0.6 fedora 21 k fedora-release-identity-basic noarch 38-0.6 fedora 11 k fedora-repos noarch 38-0.3 fedora 10 k fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k file-libs x86_64 5.42-4.fc37 fedora 676 k filesystem x86_64 3.18-2.fc37 fedora 1.1 M findutils x86_64 1:4.9.0-2.fc37 fedora 492 k gawk x86_64 5.1.1-4.fc37 fedora 1.0 M gdbm-libs x86_64 1:1.23-2.fc37 fedora 56 k glib2 x86_64 2.74.1-2.fc38 fedora 2.7 M glibc x86_64 2.36.9000-18.fc38 fedora 2.1 M glibc-common x86_64 2.36.9000-18.fc38 fedora 309 k glibc-minimal-langpack x86_64 2.36.9000-18.fc38 fedora 30 k gmp x86_64 1:6.2.1-3.fc37 fedora 315 k gnupg2 x86_64 2.3.8-1.fc38 fedora 2.6 M gnutls x86_64 3.7.8-9.fc38 fedora 1.1 M gpgme x86_64 1.17.1-3.fc38 fedora 210 k grep x86_64 3.8-1.fc38 fedora 292 k ima-evm-utils x86_64 1.4-6.fc37 fedora 63 k json-c x86_64 0.16-3.fc38 fedora 41 k keyutils-libs x86_64 1.6.1-5.fc37 fedora 31 k krb5-libs x86_64 1.20.1-3.fc38 fedora 723 k libacl x86_64 2.3.1-4.fc38 copr_base 24 k libarchive x86_64 3.6.1-3.fc38 fedora 397 k libassuan x86_64 2.5.5-5.fc37 fedora 67 k libattr x86_64 2.5.1-5.fc38 copr_base 18 k libb2 x86_64 0.98.1-7.fc37 fedora 25 k libblkid x86_64 2.38.1-3.fc38 fedora 106 k libbrotli x86_64 1.0.9-9.fc37 fedora 315 k libcap x86_64 2.48-5.fc37 fedora 67 k libcap-ng x86_64 0.8.3-4.fc38 fedora 32 k libcom_err x86_64 1.46.5-3.fc37 fedora 25 k libcomps x86_64 0.1.18-4.fc37 fedora 76 k libcurl x86_64 7.87.0-1.fc38 fedora 301 k libdnf x86_64 0.68.0-1.fc38 fedora 673 k libevent x86_64 2.1.12-7.fc37 fedora 261 k libffi x86_64 3.4.4-1.fc38 fedora 38 k libfsverity x86_64 1.4-8.fc37 fedora 19 k libgcc x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 93 k libgcrypt x86_64 1.10.1-6.fc38 fedora 511 k libgomp x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 300 k libgpg-error x86_64 1.46-1.fc38 fedora 227 k libidn2 x86_64 2.3.4-1.fc38 fedora 160 k libksba x86_64 1.6.3-1.fc38 fedora 158 k libmodulemd x86_64 2.14.0-4.fc37 fedora 234 k libmount x86_64 2.38.1-3.fc38 fedora 135 k libnghttp2 x86_64 1.51.0-1.fc38 fedora 75 k libnsl2 x86_64 2.0.0-4.fc37 fedora 30 k libpsl x86_64 0.21.1-6.fc37 fedora 63 k librepo x86_64 1.15.1-1.fc38 fedora 96 k libreport-filesystem noarch 2.17.6-1.fc38 fedora 14 k libselinux x86_64 3.4-6.fc38 fedora 86 k libsemanage x86_64 3.4-6.fc38 fedora 120 k libsepol x86_64 3.4-4.fc38 fedora 322 k libsigsegv x86_64 2.14-3.fc37 fedora 27 k libsmartcols x86_64 2.38.1-3.fc38 fedora 64 k libsolv x86_64 0.7.22-3.fc37 fedora 405 k libssh x86_64 0.10.4-2.fc38 fedora 209 k libssh-config noarch 0.10.4-2.fc38 fedora 8.8 k libstdc++ x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 799 k libtasn1 x86_64 4.19.0-1.fc38 fedora 75 k libtirpc x86_64 1.3.3-0.fc37 fedora 93 k libunistring x86_64 1.0-2.fc37 fedora 549 k libuuid x86_64 2.38.1-3.fc38 fedora 27 k libverto x86_64 0.3.2-4.fc37 fedora 21 k libxcrypt x86_64 4.4.33-5.fc38 fedora 120 k libxml2 x86_64 2.10.3-2.fc38 fedora 705 k libyaml x86_64 0.2.5-8.fc37 fedora 60 k libzstd x86_64 1.5.2-3.fc37 fedora 294 k lua-libs x86_64 5.4.4-6.fc38 fedora 131 k lz4-libs x86_64 1.9.3-5.fc37 fedora 70 k mpdecimal x86_64 2.5.1-4.fc37 fedora 102 k mpfr x86_64 4.1.1-2.fc38 fedora 598 k ncurses-base noarch 6.3-5.20221126.fc38 fedora 86 k ncurses-libs x86_64 6.3-5.20221126.fc38 fedora 329 k nettle x86_64 3.8-2.fc37 fedora 414 k npth x86_64 1.6-10.fc38 fedora 24 k openldap x86_64 2.6.3-1.fc38 fedora 254 k openssl-libs x86_64 1:3.0.5-6.fc38 fedora 2.1 M p11-kit x86_64 0.24.1-5.fc38 fedora 376 k p11-kit-trust x86_64 0.24.1-5.fc38 fedora 137 k pcre2 x86_64 10.40-1.fc37.1 fedora 236 k pcre2-syntax noarch 10.40-1.fc37.1 fedora 142 k popt x86_64 1.19-1.fc38 fedora 66 k publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k python-pip-wheel noarch 22.3.1-1.fc38 fedora 1.4 M python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k python3 x86_64 3.11.1-1.fc38 fedora 27 k python3-dateutil noarch 1:2.8.2-4.fc37 fedora 361 k python3-dbus x86_64 1.3.2-1.fc38 fedora 157 k python3-distro noarch 1.8.0-1.fc38 fedora 49 k python3-dnf noarch 4.14.0-1.fc38 fedora 607 k python3-dnf-plugins-core noarch 4.3.1-1.fc38 fedora 277 k python3-gpg x86_64 1.17.1-3.fc38 fedora 296 k python3-hawkey x86_64 0.68.0-1.fc38 fedora 108 k python3-libcomps x86_64 0.1.18-4.fc37 fedora 48 k python3-libdnf x86_64 0.68.0-1.fc38 fedora 818 k python3-libs x86_64 3.11.1-1.fc38 fedora 9.6 M python3-rpm x86_64 4.18.0-8.fc38 fedora 94 k python3-six noarch 1.16.0-8.fc37 fedora 42 k readline x86_64 8.2-2.fc38 fedora 211 k rpm x86_64 4.18.0-8.fc38 fedora 572 k rpm-build-libs x86_64 4.18.0-8.fc38 fedora 94 k rpm-libs x86_64 4.18.0-8.fc38 fedora 309 k rpm-sequoia x86_64 1.2.0-1.fc38 fedora 829 k rpm-sign-libs x86_64 4.18.0-8.fc38 fedora 27 k sed x86_64 4.8-11.fc37 fedora 306 k setup noarch 2.14.3-1.fc38 fedora 152 k shadow-utils x86_64 2:4.13-3.fc38 fedora 1.3 M sqlite-libs x86_64 3.40.0-1.fc38 fedora 661 k systemd-libs x86_64 252.4-598.fc38 fedora 632 k tpm2-tss x86_64 4.0.0-0.1.rc2.fc38 fedora 710 k tzdata noarch 2022g-1.fc38 fedora 716 k xz-libs x86_64 5.2.9-1.fc38 fedora 93 k zchunk-libs x86_64 1.2.3-1.fc38 fedora 51 k zlib x86_64 1.2.13-1.fc38 fedora 94 k Transaction Summary ========================================================================================================================= Install 137 Packages Total download size: 57 M Installed size: 200 M Downloading Packages: (1/137): audit-libs-3.0.9-1.fc38.x86_64.rpm 1.9 MB/s | 117 kB 00:00 (2/137): libacl-2.3.1-4.fc38.x86_64.rpm 395 kB/s | 24 kB 00:00 (3/137): libattr-2.5.1-5.fc38.x86_64.rpm 12 MB/s | 18 kB 00:00 (4/137): bash-5.2.9-3.fc38.x86_64.rpm 27 MB/s | 1.8 MB 00:00 (5/137): libgcc-13.0.0-0.4.fc38.x86_64.rpm 778 kB/s | 93 kB 00:00 (6/137): libgomp-13.0.0-0.4.fc38.x86_64.rpm 1.8 MB/s | 300 kB 00:00 (7/137): libstdc++-13.0.0-0.4.fc38.x86_64.rpm 3.5 MB/s | 799 kB 00:00 (8/137): alternatives-1.21-1.fc38.x86_64.rpm 250 kB/s | 38 kB 00:00 (9/137): basesystem-11-14.fc37.noarch.rpm 63 kB/s | 7.0 kB 00:00 (10/137): bzip2-libs-1.0.8-12.fc37.x86_64.rpm 340 kB/s | 41 kB 00:00 (11/137): ca-certificates-2022.2.54-5.fc37.noar 5.6 MB/s | 829 kB 00:00 (12/137): crypto-policies-20221215-1.gita4c31a3 3.6 MB/s | 90 kB 00:00 (13/137): coreutils-9.1-8.fc38.x86_64.rpm 5.2 MB/s | 1.1 MB 00:00 (14/137): curl-7.87.0-1.fc38.x86_64.rpm 8.3 MB/s | 344 kB 00:00 (15/137): dbus-libs-1.14.4-1.fc38.x86_64.rpm 4.6 MB/s | 156 kB 00:00 (16/137): cyrus-sasl-lib-2.1.28-8.fc38.x86_64.r 12 MB/s | 792 kB 00:00 (17/137): dnf-4.14.0-1.fc38.noarch.rpm 9.5 MB/s | 480 kB 00:00 (18/137): coreutils-common-9.1-8.fc38.x86_64.rp 9.5 MB/s | 2.0 MB 00:00 (19/137): dnf-data-4.14.0-1.fc38.noarch.rpm 1.8 MB/s | 43 kB 00:00 (20/137): elfutils-default-yama-scope-0.188-3.f 639 kB/s | 15 kB 00:00 (21/137): dnf-plugins-core-4.3.1-1.fc38.noarch. 1.1 MB/s | 34 kB 00:00 (22/137): elfutils-libelf-0.188-3.fc38.x86_64.r 7.1 MB/s | 196 kB 00:00 (23/137): expat-2.5.0-1.fc38.x86_64.rpm 4.0 MB/s | 110 kB 00:00 (24/137): elfutils-libs-0.188-3.fc38.x86_64.rpm 8.2 MB/s | 257 kB 00:00 (25/137): fedora-gpg-keys-38-0.3.noarch.rpm 4.4 MB/s | 125 kB 00:00 (26/137): fedora-release-38-0.6.noarch.rpm 465 kB/s | 11 kB 00:00 (27/137): fedora-release-identity-basic-38-0.6. 524 kB/s | 11 kB 00:00 (28/137): fedora-release-common-38-0.6.noarch.r 927 kB/s | 21 kB 00:00 (29/137): fedora-repos-rawhide-38-0.3.noarch.rp 451 kB/s | 9.7 kB 00:00 (30/137): fedora-repos-38-0.3.noarch.rpm 446 kB/s | 10 kB 00:00 (31/137): file-libs-5.42-4.fc37.x86_64.rpm 20 MB/s | 676 kB 00:00 (32/137): findutils-4.9.0-2.fc37.x86_64.rpm 12 MB/s | 492 kB 00:00 (33/137): filesystem-3.18-2.fc37.x86_64.rpm 19 MB/s | 1.1 MB 00:00 (34/137): gawk-5.1.1-4.fc37.x86_64.rpm 20 MB/s | 1.0 MB 00:00 (35/137): gdbm-libs-1.23-2.fc37.x86_64.rpm 2.4 MB/s | 56 kB 00:00 (36/137): glibc-common-2.36.9000-18.fc38.x86_64 8.0 MB/s | 309 kB 00:00 (37/137): glibc-minimal-langpack-2.36.9000-18.f 1.2 MB/s | 30 kB 00:00 (38/137): gmp-6.2.1-3.fc37.x86_64.rpm 7.1 MB/s | 315 kB 00:00 (39/137): glibc-2.36.9000-18.fc38.x86_64.rpm 15 MB/s | 2.1 MB 00:00 (40/137): glib2-2.74.1-2.fc38.x86_64.rpm 15 MB/s | 2.7 MB 00:00 (41/137): gpgme-1.17.1-3.fc38.x86_64.rpm 5.5 MB/s | 210 kB 00:00 (42/137): gnutls-3.7.8-9.fc38.x86_64.rpm 13 MB/s | 1.1 MB 00:00 (43/137): grep-3.8-1.fc38.x86_64.rpm 7.3 MB/s | 292 kB 00:00 (44/137): ima-evm-utils-1.4-6.fc37.x86_64.rpm 2.3 MB/s | 63 kB 00:00 (45/137): json-c-0.16-3.fc38.x86_64.rpm 1.6 MB/s | 41 kB 00:00 (46/137): 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imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-2.fc37.x86_64 1/1 Preparing : 1/1 Installing : libgcc-13.0.0-0.4.fc38.x86_64 1/137 Running scriptlet: libgcc-13.0.0-0.4.fc38.x86_64 1/137 Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/137 Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/137 Installing : tzdata-2022g-1.fc38.noarch 3/137 Installing : fedora-release-identity-basic-38-0.6.noarch 4/137 Installing : python-setuptools-wheel-65.5.1-1.fc38.noarch 5/137 Installing : publicsuffix-list-dafsa-20221208-1.fc38.noarch 6/137 Installing : pcre2-syntax-10.40-1.fc37.1.noarch 7/137 Installing : ncurses-base-6.3-5.20221126.fc38.noarch 8/137 Installing : libssh-config-0.10.4-2.fc38.noarch 9/137 Installing : libreport-filesystem-2.17.6-1.fc38.noarch 10/137 Installing : dnf-data-4.14.0-1.fc38.noarch 11/137 warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew Installing : fedora-gpg-keys-38-0.3.noarch 12/137 Installing : 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scriptlet: dnf-4.14.0-1.fc38.noarch 136/137 Running scriptlet: rpm-4.18.0-8.fc38.x86_64 137/137 Installing : rpm-4.18.0-8.fc38.x86_64 137/137 Running scriptlet: filesystem-3.18-2.fc37.x86_64 137/137 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 137/137 Running scriptlet: rpm-4.18.0-8.fc38.x86_64 137/137 Verifying : audit-libs-3.0.9-1.fc38.x86_64 1/137 Verifying : bash-5.2.9-3.fc38.x86_64 2/137 Verifying : libacl-2.3.1-4.fc38.x86_64 3/137 Verifying : libattr-2.5.1-5.fc38.x86_64 4/137 Verifying : libgcc-13.0.0-0.4.fc38.x86_64 5/137 Verifying : libgomp-13.0.0-0.4.fc38.x86_64 6/137 Verifying : libstdc++-13.0.0-0.4.fc38.x86_64 7/137 Verifying : alternatives-1.21-1.fc38.x86_64 8/137 Verifying : basesystem-11-14.fc37.noarch 9/137 Verifying : bzip2-libs-1.0.8-12.fc37.x86_64 10/137 Verifying : ca-certificates-2022.2.54-5.fc37.noarch 11/137 Verifying : coreutils-9.1-8.fc38.x86_64 12/137 Verifying : coreutils-common-9.1-8.fc38.x86_64 13/137 Verifying : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 14/137 Verifying : curl-7.87.0-1.fc38.x86_64 15/137 Verifying : cyrus-sasl-lib-2.1.28-8.fc38.x86_64 16/137 Verifying : dbus-libs-1:1.14.4-1.fc38.x86_64 17/137 Verifying : dnf-4.14.0-1.fc38.noarch 18/137 Verifying : dnf-data-4.14.0-1.fc38.noarch 19/137 Verifying : dnf-plugins-core-4.3.1-1.fc38.noarch 20/137 Verifying : elfutils-default-yama-scope-0.188-3.fc38.noarch 21/137 Verifying : elfutils-libelf-0.188-3.fc38.x86_64 22/137 Verifying : elfutils-libs-0.188-3.fc38.x86_64 23/137 Verifying : expat-2.5.0-1.fc38.x86_64 24/137 Verifying : fedora-gpg-keys-38-0.3.noarch 25/137 Verifying : fedora-release-38-0.6.noarch 26/137 Verifying : fedora-release-common-38-0.6.noarch 27/137 Verifying : fedora-release-identity-basic-38-0.6.noarch 28/137 Verifying : fedora-repos-38-0.3.noarch 29/137 Verifying : fedora-repos-rawhide-38-0.3.noarch 30/137 Verifying : file-libs-5.42-4.fc37.x86_64 31/137 Verifying : filesystem-3.18-2.fc37.x86_64 32/137 Verifying : findutils-1:4.9.0-2.fc37.x86_64 33/137 Verifying : gawk-5.1.1-4.fc37.x86_64 34/137 Verifying : gdbm-libs-1:1.23-2.fc37.x86_64 35/137 Verifying : glib2-2.74.1-2.fc38.x86_64 36/137 Verifying : glibc-2.36.9000-18.fc38.x86_64 37/137 Verifying : glibc-common-2.36.9000-18.fc38.x86_64 38/137 Verifying : glibc-minimal-langpack-2.36.9000-18.fc38.x86_64 39/137 Verifying : gmp-1:6.2.1-3.fc37.x86_64 40/137 Verifying : gnupg2-2.3.8-1.fc38.x86_64 41/137 Verifying : gnutls-3.7.8-9.fc38.x86_64 42/137 Verifying : gpgme-1.17.1-3.fc38.x86_64 43/137 Verifying : grep-3.8-1.fc38.x86_64 44/137 Verifying : ima-evm-utils-1.4-6.fc37.x86_64 45/137 Verifying : json-c-0.16-3.fc38.x86_64 46/137 Verifying : keyutils-libs-1.6.1-5.fc37.x86_64 47/137 Verifying : krb5-libs-1.20.1-3.fc38.x86_64 48/137 Verifying : libarchive-3.6.1-3.fc38.x86_64 49/137 Verifying : libassuan-2.5.5-5.fc37.x86_64 50/137 Verifying : libb2-0.98.1-7.fc37.x86_64 51/137 Verifying : libblkid-2.38.1-3.fc38.x86_64 52/137 Verifying : libbrotli-1.0.9-9.fc37.x86_64 53/137 Verifying : libcap-2.48-5.fc37.x86_64 54/137 Verifying : libcap-ng-0.8.3-4.fc38.x86_64 55/137 Verifying : libcom_err-1.46.5-3.fc37.x86_64 56/137 Verifying : libcomps-0.1.18-4.fc37.x86_64 57/137 Verifying : libcurl-7.87.0-1.fc38.x86_64 58/137 Verifying : libdnf-0.68.0-1.fc38.x86_64 59/137 Verifying : libevent-2.1.12-7.fc37.x86_64 60/137 Verifying : libffi-3.4.4-1.fc38.x86_64 61/137 Verifying : libfsverity-1.4-8.fc37.x86_64 62/137 Verifying : libgcrypt-1.10.1-6.fc38.x86_64 63/137 Verifying : libgpg-error-1.46-1.fc38.x86_64 64/137 Verifying : libidn2-2.3.4-1.fc38.x86_64 65/137 Verifying : libksba-1.6.3-1.fc38.x86_64 66/137 Verifying : libmodulemd-2.14.0-4.fc37.x86_64 67/137 Verifying : libmount-2.38.1-3.fc38.x86_64 68/137 Verifying : libnghttp2-1.51.0-1.fc38.x86_64 69/137 Verifying : libnsl2-2.0.0-4.fc37.x86_64 70/137 Verifying : libpsl-0.21.1-6.fc37.x86_64 71/137 Verifying : librepo-1.15.1-1.fc38.x86_64 72/137 Verifying : libreport-filesystem-2.17.6-1.fc38.noarch 73/137 Verifying : libselinux-3.4-6.fc38.x86_64 74/137 Verifying : libsemanage-3.4-6.fc38.x86_64 75/137 Verifying : libsepol-3.4-4.fc38.x86_64 76/137 Verifying : libsigsegv-2.14-3.fc37.x86_64 77/137 Verifying : libsmartcols-2.38.1-3.fc38.x86_64 78/137 Verifying : libsolv-0.7.22-3.fc37.x86_64 79/137 Verifying : libssh-0.10.4-2.fc38.x86_64 80/137 Verifying : libssh-config-0.10.4-2.fc38.noarch 81/137 Verifying : libtasn1-4.19.0-1.fc38.x86_64 82/137 Verifying : libtirpc-1.3.3-0.fc37.x86_64 83/137 Verifying : libunistring-1.0-2.fc37.x86_64 84/137 Verifying : libuuid-2.38.1-3.fc38.x86_64 85/137 Verifying : libverto-0.3.2-4.fc37.x86_64 86/137 Verifying : libxcrypt-4.4.33-5.fc38.x86_64 87/137 Verifying : libxml2-2.10.3-2.fc38.x86_64 88/137 Verifying : libyaml-0.2.5-8.fc37.x86_64 89/137 Verifying : libzstd-1.5.2-3.fc37.x86_64 90/137 Verifying : lua-libs-5.4.4-6.fc38.x86_64 91/137 Verifying : lz4-libs-1.9.3-5.fc37.x86_64 92/137 Verifying : mpdecimal-2.5.1-4.fc37.x86_64 93/137 Verifying : mpfr-4.1.1-2.fc38.x86_64 94/137 Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 95/137 Verifying : ncurses-libs-6.3-5.20221126.fc38.x86_64 96/137 Verifying : nettle-3.8-2.fc37.x86_64 97/137 Verifying : npth-1.6-10.fc38.x86_64 98/137 Verifying : openldap-2.6.3-1.fc38.x86_64 99/137 Verifying : openssl-libs-1:3.0.5-6.fc38.x86_64 100/137 Verifying : p11-kit-0.24.1-5.fc38.x86_64 101/137 Verifying : p11-kit-trust-0.24.1-5.fc38.x86_64 102/137 Verifying : pcre2-10.40-1.fc37.1.x86_64 103/137 Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 104/137 Verifying : popt-1.19-1.fc38.x86_64 105/137 Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 106/137 Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 107/137 Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 108/137 Verifying : python3-3.11.1-1.fc38.x86_64 109/137 Verifying : python3-dateutil-1:2.8.2-4.fc37.noarch 110/137 Verifying : python3-dbus-1.3.2-1.fc38.x86_64 111/137 Verifying : python3-distro-1.8.0-1.fc38.noarch 112/137 Verifying : python3-dnf-4.14.0-1.fc38.noarch 113/137 Verifying : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 114/137 Verifying : python3-gpg-1.17.1-3.fc38.x86_64 115/137 Verifying : python3-hawkey-0.68.0-1.fc38.x86_64 116/137 Verifying : python3-libcomps-0.1.18-4.fc37.x86_64 117/137 Verifying : python3-libdnf-0.68.0-1.fc38.x86_64 118/137 Verifying : python3-libs-3.11.1-1.fc38.x86_64 119/137 Verifying : python3-rpm-4.18.0-8.fc38.x86_64 120/137 Verifying : python3-six-1.16.0-8.fc37.noarch 121/137 Verifying : readline-8.2-2.fc38.x86_64 122/137 Verifying : rpm-4.18.0-8.fc38.x86_64 123/137 Verifying : rpm-build-libs-4.18.0-8.fc38.x86_64 124/137 Verifying : rpm-libs-4.18.0-8.fc38.x86_64 125/137 Verifying : rpm-sequoia-1.2.0-1.fc38.x86_64 126/137 Verifying : rpm-sign-libs-4.18.0-8.fc38.x86_64 127/137 Verifying : sed-4.8-11.fc37.x86_64 128/137 Verifying : setup-2.14.3-1.fc38.noarch 129/137 Verifying : shadow-utils-2:4.13-3.fc38.x86_64 130/137 Verifying : sqlite-libs-3.40.0-1.fc38.x86_64 131/137 Verifying : systemd-libs-252.4-598.fc38.x86_64 132/137 Verifying : tpm2-tss-4.0.0-0.1.rc2.fc38.x86_64 133/137 Verifying : tzdata-2022g-1.fc38.noarch 134/137 Verifying : xz-libs-5.2.9-1.fc38.x86_64 135/137 Verifying : zchunk-libs-1.2.3-1.fc38.x86_64 136/137 Verifying : zlib-1.2.13-1.fc38.x86_64 137/137 Installed products updated. Installed: alternatives-1.21-1.fc38.x86_64 audit-libs-3.0.9-1.fc38.x86_64 basesystem-11-14.fc37.noarch bash-5.2.9-3.fc38.x86_64 bzip2-libs-1.0.8-12.fc37.x86_64 ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-8.fc38.x86_64 coreutils-common-9.1-8.fc38.x86_64 crypto-policies-20221215-1.gita4c31a3.fc38.noarch curl-7.87.0-1.fc38.x86_64 cyrus-sasl-lib-2.1.28-8.fc38.x86_64 dbus-libs-1:1.14.4-1.fc38.x86_64 dnf-4.14.0-1.fc38.noarch dnf-data-4.14.0-1.fc38.noarch dnf-plugins-core-4.3.1-1.fc38.noarch elfutils-default-yama-scope-0.188-3.fc38.noarch elfutils-libelf-0.188-3.fc38.x86_64 elfutils-libs-0.188-3.fc38.x86_64 expat-2.5.0-1.fc38.x86_64 fedora-gpg-keys-38-0.3.noarch fedora-release-38-0.6.noarch fedora-release-common-38-0.6.noarch fedora-release-identity-basic-38-0.6.noarch fedora-repos-38-0.3.noarch fedora-repos-rawhide-38-0.3.noarch file-libs-5.42-4.fc37.x86_64 filesystem-3.18-2.fc37.x86_64 findutils-1:4.9.0-2.fc37.x86_64 gawk-5.1.1-4.fc37.x86_64 gdbm-libs-1:1.23-2.fc37.x86_64 glib2-2.74.1-2.fc38.x86_64 glibc-2.36.9000-18.fc38.x86_64 glibc-common-2.36.9000-18.fc38.x86_64 glibc-minimal-langpack-2.36.9000-18.fc38.x86_64 gmp-1:6.2.1-3.fc37.x86_64 gnupg2-2.3.8-1.fc38.x86_64 gnutls-3.7.8-9.fc38.x86_64 gpgme-1.17.1-3.fc38.x86_64 grep-3.8-1.fc38.x86_64 ima-evm-utils-1.4-6.fc37.x86_64 json-c-0.16-3.fc38.x86_64 keyutils-libs-1.6.1-5.fc37.x86_64 krb5-libs-1.20.1-3.fc38.x86_64 libacl-2.3.1-4.fc38.x86_64 libarchive-3.6.1-3.fc38.x86_64 libassuan-2.5.5-5.fc37.x86_64 libattr-2.5.1-5.fc38.x86_64 libb2-0.98.1-7.fc37.x86_64 libblkid-2.38.1-3.fc38.x86_64 libbrotli-1.0.9-9.fc37.x86_64 libcap-2.48-5.fc37.x86_64 libcap-ng-0.8.3-4.fc38.x86_64 libcom_err-1.46.5-3.fc37.x86_64 libcomps-0.1.18-4.fc37.x86_64 libcurl-7.87.0-1.fc38.x86_64 libdnf-0.68.0-1.fc38.x86_64 libevent-2.1.12-7.fc37.x86_64 libffi-3.4.4-1.fc38.x86_64 libfsverity-1.4-8.fc37.x86_64 libgcc-13.0.0-0.4.fc38.x86_64 libgcrypt-1.10.1-6.fc38.x86_64 libgomp-13.0.0-0.4.fc38.x86_64 libgpg-error-1.46-1.fc38.x86_64 libidn2-2.3.4-1.fc38.x86_64 libksba-1.6.3-1.fc38.x86_64 libmodulemd-2.14.0-4.fc37.x86_64 libmount-2.38.1-3.fc38.x86_64 libnghttp2-1.51.0-1.fc38.x86_64 libnsl2-2.0.0-4.fc37.x86_64 libpsl-0.21.1-6.fc37.x86_64 librepo-1.15.1-1.fc38.x86_64 libreport-filesystem-2.17.6-1.fc38.noarch libselinux-3.4-6.fc38.x86_64 libsemanage-3.4-6.fc38.x86_64 libsepol-3.4-4.fc38.x86_64 libsigsegv-2.14-3.fc37.x86_64 libsmartcols-2.38.1-3.fc38.x86_64 libsolv-0.7.22-3.fc37.x86_64 libssh-0.10.4-2.fc38.x86_64 libssh-config-0.10.4-2.fc38.noarch libstdc++-13.0.0-0.4.fc38.x86_64 libtasn1-4.19.0-1.fc38.x86_64 libtirpc-1.3.3-0.fc37.x86_64 libunistring-1.0-2.fc37.x86_64 libuuid-2.38.1-3.fc38.x86_64 libverto-0.3.2-4.fc37.x86_64 libxcrypt-4.4.33-5.fc38.x86_64 libxml2-2.10.3-2.fc38.x86_64 libyaml-0.2.5-8.fc37.x86_64 libzstd-1.5.2-3.fc37.x86_64 lua-libs-5.4.4-6.fc38.x86_64 lz4-libs-1.9.3-5.fc37.x86_64 mpdecimal-2.5.1-4.fc37.x86_64 mpfr-4.1.1-2.fc38.x86_64 ncurses-base-6.3-5.20221126.fc38.noarch ncurses-libs-6.3-5.20221126.fc38.x86_64 nettle-3.8-2.fc37.x86_64 npth-1.6-10.fc38.x86_64 openldap-2.6.3-1.fc38.x86_64 openssl-libs-1:3.0.5-6.fc38.x86_64 p11-kit-0.24.1-5.fc38.x86_64 p11-kit-trust-0.24.1-5.fc38.x86_64 pcre2-10.40-1.fc37.1.x86_64 pcre2-syntax-10.40-1.fc37.1.noarch popt-1.19-1.fc38.x86_64 publicsuffix-list-dafsa-20221208-1.fc38.noarch python-pip-wheel-22.3.1-1.fc38.noarch python-setuptools-wheel-65.5.1-1.fc38.noarch python3-3.11.1-1.fc38.x86_64 python3-dateutil-1:2.8.2-4.fc37.noarch python3-dbus-1.3.2-1.fc38.x86_64 python3-distro-1.8.0-1.fc38.noarch python3-dnf-4.14.0-1.fc38.noarch python3-dnf-plugins-core-4.3.1-1.fc38.noarch python3-gpg-1.17.1-3.fc38.x86_64 python3-hawkey-0.68.0-1.fc38.x86_64 python3-libcomps-0.1.18-4.fc37.x86_64 python3-libdnf-0.68.0-1.fc38.x86_64 python3-libs-3.11.1-1.fc38.x86_64 python3-rpm-4.18.0-8.fc38.x86_64 python3-six-1.16.0-8.fc37.noarch readline-8.2-2.fc38.x86_64 rpm-4.18.0-8.fc38.x86_64 rpm-build-libs-4.18.0-8.fc38.x86_64 rpm-libs-4.18.0-8.fc38.x86_64 rpm-sequoia-1.2.0-1.fc38.x86_64 rpm-sign-libs-4.18.0-8.fc38.x86_64 sed-4.8-11.fc37.x86_64 setup-2.14.3-1.fc38.noarch shadow-utils-2:4.13-3.fc38.x86_64 sqlite-libs-3.40.0-1.fc38.x86_64 systemd-libs-252.4-598.fc38.x86_64 tpm2-tss-4.0.0-0.1.rc2.fc38.x86_64 tzdata-2022g-1.fc38.noarch xz-libs-5.2.9-1.fc38.x86_64 zchunk-libs-1.2.3-1.fc38.x86_64 zlib-1.2.13-1.fc38.x86_64 Complete! Finish(bootstrap): dnf install 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-x86_64-1671795578.114598/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 Mock Version: 3.5 INFO: Mock Version: 3.5 Start: dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 13 kB/s | 3.0 kB 00:00 Copr repository 14 MB/s | 3.7 MB 00:00 Additional repo https_jakub_fedorapeople_org_fe 11 kB/s | 3.0 kB 00:00 fedora 85 kB/s | 23 kB 00:00 Dependencies resolved. ========================================================================================================================= Package Arch Version Repository Size ========================================================================================================================= Installing group/module packages: bash x86_64 5.2.9-3.fc38 copr_base 1.8 M bzip2 x86_64 1.0.8-12.fc37 fedora 52 k coreutils x86_64 9.1-8.fc38 fedora 1.1 M cpio x86_64 2.13-13.fc38 fedora 276 k diffutils x86_64 3.8-3.fc37 fedora 378 k fedora-release-common noarch 38-0.6 fedora 21 k findutils x86_64 1:4.9.0-2.fc37 fedora 492 k gawk x86_64 5.1.1-4.fc37 fedora 1.0 M glibc-minimal-langpack x86_64 2.36.9000-18.fc38 fedora 30 k grep x86_64 3.8-1.fc38 fedora 292 k gzip x86_64 1.12-2.fc37 fedora 166 k info x86_64 7.0.1-1.fc38 fedora 181 k patch x86_64 2.7.6-17.fc37 fedora 124 k redhat-rpm-config noarch 235-1.fc38 fedora 80 k rpm-build x86_64 4.18.0-8.fc38 fedora 77 k sed x86_64 4.8-11.fc37 fedora 306 k shadow-utils x86_64 2:4.13-3.fc38 fedora 1.3 M tar x86_64 2:1.34-5.fc38 fedora 885 k unzip x86_64 6.0-58.fc38 fedora 182 k util-linux x86_64 2.38.1-3.fc38 fedora 2.3 M which x86_64 2.21-36.fc38 fedora 41 k xz x86_64 5.2.9-1.fc38 fedora 306 k Installing dependencies: alternatives x86_64 1.21-1.fc38 fedora 38 k ansible-srpm-macros noarch 1-8.1.fc38 fedora 8.6 k audit-libs x86_64 3.0.9-1.fc38 copr_base 117 k authselect x86_64 1.4.2-1.fc38 copr_base 140 k authselect-libs x86_64 1.4.2-1.fc38 copr_base 237 k basesystem noarch 11-14.fc37 fedora 7.0 k binutils x86_64 2.39-6.fc38 fedora 5.5 M binutils-gold x86_64 2.39-6.fc38 fedora 777 k bzip2-libs x86_64 1.0.8-12.fc37 fedora 41 k ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k coreutils-common x86_64 9.1-8.fc38 fedora 2.0 M cracklib x86_64 2.9.7-30.fc38 fedora 92 k crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k curl x86_64 7.87.0-1.fc38 fedora 344 k cyrus-sasl-lib x86_64 2.1.28-8.fc38 fedora 792 k debugedit x86_64 5.0-5.fc37 fedora 77 k dwz x86_64 0.15-1.fc38 fedora 136 k ed x86_64 1.18-2.fc37 fedora 78 k efi-srpm-macros noarch 5-6.fc37 fedora 22 k elfutils x86_64 0.188-3.fc38 fedora 529 k elfutils-debuginfod-client x86_64 0.188-3.fc38 fedora 40 k elfutils-default-yama-scope noarch 0.188-3.fc38 fedora 15 k elfutils-libelf x86_64 0.188-3.fc38 fedora 196 k elfutils-libs x86_64 0.188-3.fc38 fedora 257 k fedora-gpg-keys noarch 38-0.3 fedora 125 k fedora-release noarch 38-0.6 fedora 11 k fedora-release-identity-basic noarch 38-0.6 fedora 11 k fedora-repos noarch 38-0.3 fedora 10 k fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k file x86_64 5.42-4.fc37 fedora 49 k file-libs x86_64 5.42-4.fc37 fedora 676 k filesystem x86_64 3.18-2.fc37 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-10.fc38 fedora 26 k fpc-srpm-macros noarch 1.3-6.fc37 fedora 7.7 k gdb-minimal x86_64 12.1-10.fc38 fedora 3.7 M gdbm-libs x86_64 1:1.23-2.fc37 fedora 56 k ghc-srpm-macros noarch 1.5.0-7.fc37 fedora 7.8 k glibc x86_64 2.36.9000-18.fc38 fedora 2.1 M glibc-common x86_64 2.36.9000-18.fc38 fedora 309 k glibc-gconv-extra x86_64 2.36.9000-18.fc38 fedora 1.6 M gmp x86_64 1:6.2.1-3.fc37 fedora 315 k gnat-srpm-macros noarch 4-16.fc37 fedora 8.3 k go-srpm-macros noarch 3.2.0-1.fc38 fedora 27 k jansson x86_64 2.13.1-5.fc37 fedora 44 k kernel-srpm-macros noarch 1.0-15.fc37 fedora 9.4 k keyutils-libs x86_64 1.6.1-5.fc37 fedora 31 k krb5-libs x86_64 1.20.1-3.fc38 fedora 723 k libacl x86_64 2.3.1-4.fc38 copr_base 24 k libarchive x86_64 3.6.1-3.fc38 fedora 397 k libattr x86_64 2.5.1-5.fc38 copr_base 18 k libblkid x86_64 2.38.1-3.fc38 fedora 106 k libbrotli x86_64 1.0.9-9.fc37 fedora 315 k libcap x86_64 2.48-5.fc37 fedora 67 k libcap-ng x86_64 0.8.3-4.fc38 fedora 32 k libcom_err x86_64 1.46.5-3.fc37 fedora 25 k libcurl x86_64 7.87.0-1.fc38 fedora 301 k libdb x86_64 5.3.28-54.fc38 fedora 764 k libeconf x86_64 0.4.0-4.fc37 fedora 27 k libevent x86_64 2.1.12-7.fc37 fedora 261 k libfdisk x86_64 2.38.1-3.fc38 fedora 160 k libffi x86_64 3.4.4-1.fc38 fedora 38 k libgcc x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 93 k libgomp x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 300 k libidn2 x86_64 2.3.4-1.fc38 fedora 160 k libmount x86_64 2.38.1-3.fc38 fedora 135 k libnghttp2 x86_64 1.51.0-1.fc38 fedora 75 k libnsl2 x86_64 2.0.0-4.fc37 fedora 30 k libpkgconf x86_64 1.8.0-3.fc37 fedora 36 k libpsl x86_64 0.21.1-6.fc37 fedora 63 k libpwquality x86_64 1.4.4-11.fc37 fedora 116 k libselinux x86_64 3.4-6.fc38 fedora 86 k libsemanage x86_64 3.4-6.fc38 fedora 120 k libsepol x86_64 3.4-4.fc38 fedora 322 k libsigsegv x86_64 2.14-3.fc37 fedora 27 k libsmartcols x86_64 2.38.1-3.fc38 fedora 64 k libssh x86_64 0.10.4-2.fc38 fedora 209 k libssh-config noarch 0.10.4-2.fc38 fedora 8.8 k libstdc++ x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 799 k libtasn1 x86_64 4.19.0-1.fc38 fedora 75 k libtirpc x86_64 1.3.3-0.fc37 fedora 93 k libunistring x86_64 1.0-2.fc37 fedora 549 k libutempter x86_64 1.2.1-7.fc37 fedora 26 k libuuid x86_64 2.38.1-3.fc38 fedora 27 k libverto x86_64 0.3.2-4.fc37 fedora 21 k libxcrypt x86_64 4.4.33-5.fc38 fedora 120 k libxml2 x86_64 2.10.3-2.fc38 fedora 705 k libzstd x86_64 1.5.2-3.fc37 fedora 294 k lua-libs x86_64 5.4.4-6.fc38 fedora 131 k lua-srpm-macros noarch 1-7.fc37 fedora 8.8 k lz4-libs x86_64 1.9.3-5.fc37 fedora 70 k mpfr x86_64 4.1.1-2.fc38 fedora 598 k ncurses-base noarch 6.3-5.20221126.fc38 fedora 86 k ncurses-libs x86_64 6.3-5.20221126.fc38 fedora 329 k nettle x86_64 3.8-2.fc37 fedora 414 k nim-srpm-macros noarch 3-7.fc37 fedora 8.4 k ocaml-srpm-macros noarch 7-2.fc37 fedora 13 k openblas-srpm-macros noarch 2-12.fc37 fedora 7.5 k openldap x86_64 2.6.3-1.fc38 fedora 254 k openssl-libs x86_64 1:3.0.5-6.fc38 fedora 2.1 M p11-kit x86_64 0.24.1-5.fc38 fedora 376 k p11-kit-trust x86_64 0.24.1-5.fc38 fedora 137 k package-notes-srpm-macros noarch 0.5-6.fc38 fedora 11 k pam x86_64 1.5.2-15.fc38 fedora 559 k pam-libs x86_64 1.5.2-15.fc38 fedora 57 k pcre2 x86_64 10.40-1.fc37.1 fedora 236 k pcre2-syntax noarch 10.40-1.fc37.1 fedora 142 k perl-srpm-macros noarch 1-47.fc38 fedora 8.2 k pkgconf x86_64 1.8.0-3.fc37 fedora 41 k pkgconf-m4 noarch 1.8.0-3.fc37 fedora 14 k pkgconf-pkg-config x86_64 1.8.0-3.fc37 fedora 10 k popt x86_64 1.19-1.fc38 fedora 66 k publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k python-srpm-macros noarch 3.11-6.fc38 fedora 25 k qt5-srpm-macros noarch 5.15.7-1.fc38 fedora 7.9 k readline x86_64 8.2-2.fc38 fedora 211 k rpm x86_64 4.18.0-8.fc38 fedora 572 k rpm-build-libs x86_64 4.18.0-8.fc38 fedora 94 k rpm-libs x86_64 4.18.0-8.fc38 fedora 309 k rpm-sequoia x86_64 1.2.0-1.fc38 fedora 829 k rpmautospec-rpm-macros noarch 0.3.1-1.fc38 fedora 8.8 k rust-srpm-macros noarch 23-1.fc38 fedora 9.4 k setup noarch 2.14.3-1.fc38 fedora 152 k sqlite-libs x86_64 3.40.0-1.fc38 fedora 661 k systemd-libs x86_64 252.4-598.fc38 fedora 632 k tzdata noarch 2022g-1.fc38 fedora 716 k util-linux-core x86_64 2.38.1-3.fc38 fedora 470 k xxhash-libs x86_64 0.8.1-3.fc37 fedora 41 k xz-libs x86_64 5.2.9-1.fc38 fedora 93 k zip x86_64 3.0-35.fc38 fedora 259 k zlib x86_64 1.2.13-1.fc38 fedora 94 k zstd x86_64 1.5.2-3.fc37 fedora 447 k Installing Groups: Buildsystem building group Transaction Summary ========================================================================================================================= Install 153 Packages Total size: 52 M Installed size: 181 M Downloading Packages: [SKIPPED] audit-libs-3.0.9-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] authselect-1.4.2-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] authselect-libs-1.4.2-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] bash-5.2.9-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libacl-2.3.1-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libattr-2.5.1-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] libgcc-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libgomp-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libstdc++-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded [SKIPPED] alternatives-1.21-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] ansible-srpm-macros-1-8.1.fc38.noarch.rpm: Already downloaded [SKIPPED] basesystem-11-14.fc37.noarch.rpm: Already downloaded [SKIPPED] binutils-2.39-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] binutils-gold-2.39-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] bzip2-1.0.8-12.fc37.x86_64.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.8-12.fc37.x86_64.rpm: Already downloaded [SKIPPED] ca-certificates-2022.2.54-5.fc37.noarch.rpm: Already downloaded [SKIPPED] coreutils-9.1-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] coreutils-common-9.1-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] cpio-2.13-13.fc38.x86_64.rpm: Already downloaded [SKIPPED] cracklib-2.9.7-30.fc38.x86_64.rpm: Already downloaded [SKIPPED] crypto-policies-20221215-1.gita4c31a3.fc38.noarch.rpm: Already downloaded [SKIPPED] curl-7.87.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] cyrus-sasl-lib-2.1.28-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] debugedit-5.0-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] diffutils-3.8-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] dwz-0.15-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] ed-1.18-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] efi-srpm-macros-5-6.fc37.noarch.rpm: Already downloaded [SKIPPED] elfutils-0.188-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-debuginfod-client-0.188-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-default-yama-scope-0.188-3.fc38.noarch.rpm: Already downloaded [SKIPPED] elfutils-libelf-0.188-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-libs-0.188-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] fedora-gpg-keys-38-0.3.noarch.rpm: Already downloaded [SKIPPED] fedora-release-38-0.6.noarch.rpm: Already downloaded [SKIPPED] fedora-release-common-38-0.6.noarch.rpm: Already downloaded [SKIPPED] fedora-release-identity-basic-38-0.6.noarch.rpm: Already downloaded [SKIPPED] fedora-repos-38-0.3.noarch.rpm: Already downloaded [SKIPPED] fedora-repos-rawhide-38-0.3.noarch.rpm: Already downloaded [SKIPPED] file-5.42-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] file-libs-5.42-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] filesystem-3.18-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] findutils-4.9.0-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] fonts-srpm-macros-2.0.5-10.fc38.noarch.rpm: Already downloaded [SKIPPED] fpc-srpm-macros-1.3-6.fc37.noarch.rpm: Already downloaded [SKIPPED] gawk-5.1.1-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] gdb-minimal-12.1-10.fc38.x86_64.rpm: Already downloaded [SKIPPED] gdbm-libs-1.23-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] ghc-srpm-macros-1.5.0-7.fc37.noarch.rpm: Already downloaded [SKIPPED] glibc-2.36.9000-18.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-common-2.36.9000-18.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-gconv-extra-2.36.9000-18.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-minimal-langpack-2.36.9000-18.fc38.x86_64.rpm: Already downloaded [SKIPPED] gmp-6.2.1-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] gnat-srpm-macros-4-16.fc37.noarch.rpm: Already downloaded [SKIPPED] go-srpm-macros-3.2.0-1.fc38.noarch.rpm: Already downloaded [SKIPPED] grep-3.8-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] gzip-1.12-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] info-7.0.1-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] jansson-2.13.1-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] kernel-srpm-macros-1.0-15.fc37.noarch.rpm: Already downloaded [SKIPPED] keyutils-libs-1.6.1-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] krb5-libs-1.20.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libarchive-3.6.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libblkid-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libbrotli-1.0.9-9.fc37.x86_64.rpm: Already downloaded [SKIPPED] libcap-2.48-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] libcap-ng-0.8.3-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libcom_err-1.46.5-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] libcurl-7.87.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libdb-5.3.28-54.fc38.x86_64.rpm: Already downloaded [SKIPPED] libeconf-0.4.0-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] libevent-2.1.12-7.fc37.x86_64.rpm: Already downloaded [SKIPPED] libfdisk-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libffi-3.4.4-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libidn2-2.3.4-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libmount-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libnghttp2-1.51.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libnsl2-2.0.0-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] libpkgconf-1.8.0-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] libpsl-0.21.1-6.fc37.x86_64.rpm: Already downloaded [SKIPPED] libpwquality-1.4.4-11.fc37.x86_64.rpm: Already downloaded [SKIPPED] libselinux-3.4-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] libsemanage-3.4-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] libsepol-3.4-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libsigsegv-2.14-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] libsmartcols-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libssh-0.10.4-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libssh-config-0.10.4-2.fc38.noarch.rpm: Already downloaded [SKIPPED] libtasn1-4.19.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libtirpc-1.3.3-0.fc37.x86_64.rpm: Already downloaded [SKIPPED] libunistring-1.0-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] libutempter-1.2.1-7.fc37.x86_64.rpm: Already downloaded [SKIPPED] libuuid-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libverto-0.3.2-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] libxcrypt-4.4.33-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] libxml2-2.10.3-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libzstd-1.5.2-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] lua-libs-5.4.4-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] lua-srpm-macros-1-7.fc37.noarch.rpm: Already downloaded [SKIPPED] lz4-libs-1.9.3-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] mpfr-4.1.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] ncurses-base-6.3-5.20221126.fc38.noarch.rpm: Already downloaded [SKIPPED] ncurses-libs-6.3-5.20221126.fc38.x86_64.rpm: Already downloaded [SKIPPED] nettle-3.8-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] nim-srpm-macros-3-7.fc37.noarch.rpm: Already downloaded [SKIPPED] ocaml-srpm-macros-7-2.fc37.noarch.rpm: Already downloaded [SKIPPED] openblas-srpm-macros-2-12.fc37.noarch.rpm: Already downloaded [SKIPPED] openldap-2.6.3-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] openssl-libs-3.0.5-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] p11-kit-0.24.1-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] p11-kit-trust-0.24.1-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] package-notes-srpm-macros-0.5-6.fc38.noarch.rpm: Already downloaded [SKIPPED] pam-1.5.2-15.fc38.x86_64.rpm: Already downloaded [SKIPPED] pam-libs-1.5.2-15.fc38.x86_64.rpm: Already downloaded [SKIPPED] patch-2.7.6-17.fc37.x86_64.rpm: Already downloaded [SKIPPED] pcre2-10.40-1.fc37.1.x86_64.rpm: Already downloaded [SKIPPED] pcre2-syntax-10.40-1.fc37.1.noarch.rpm: Already downloaded [SKIPPED] perl-srpm-macros-1-47.fc38.noarch.rpm: Already downloaded [SKIPPED] pkgconf-1.8.0-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] pkgconf-m4-1.8.0-3.fc37.noarch.rpm: Already downloaded [SKIPPED] pkgconf-pkg-config-1.8.0-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] popt-1.19-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] publicsuffix-list-dafsa-20221208-1.fc38.noarch.rpm: Already downloaded [SKIPPED] python-srpm-macros-3.11-6.fc38.noarch.rpm: Already downloaded [SKIPPED] qt5-srpm-macros-5.15.7-1.fc38.noarch.rpm: Already downloaded [SKIPPED] readline-8.2-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] redhat-rpm-config-235-1.fc38.noarch.rpm: Already downloaded [SKIPPED] rpm-4.18.0-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-build-4.18.0-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-build-libs-4.18.0-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-libs-4.18.0-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-sequoia-1.2.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpmautospec-rpm-macros-0.3.1-1.fc38.noarch.rpm: Already downloaded [SKIPPED] rust-srpm-macros-23-1.fc38.noarch.rpm: Already downloaded [SKIPPED] sed-4.8-11.fc37.x86_64.rpm: Already downloaded [SKIPPED] setup-2.14.3-1.fc38.noarch.rpm: Already downloaded [SKIPPED] shadow-utils-4.13-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] sqlite-libs-3.40.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] systemd-libs-252.4-598.fc38.x86_64.rpm: Already downloaded [SKIPPED] tar-1.34-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] tzdata-2022g-1.fc38.noarch.rpm: Already downloaded [SKIPPED] unzip-6.0-58.fc38.x86_64.rpm: Already downloaded [SKIPPED] util-linux-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] util-linux-core-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] which-2.21-36.fc38.x86_64.rpm: Already downloaded [SKIPPED] xxhash-libs-0.8.1-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] xz-5.2.9-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] xz-libs-5.2.9-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] zip-3.0-35.fc38.x86_64.rpm: Already downloaded [SKIPPED] zlib-1.2.13-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] zstd-1.5.2-3.fc37.x86_64.rpm: Already downloaded fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xEB10B464: Userid : "Fedora (38) " Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464 From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary Key imported successfully fedora 1.6 MB/s | 1.6 kB 00:00 GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x5323552A: Userid : "Fedora (37) " Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-2.fc37.x86_64 1/1 Preparing : 1/1 Installing : libgcc-13.0.0-0.4.fc38.x86_64 1/153 Running scriptlet: libgcc-13.0.0-0.4.fc38.x86_64 1/153 Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/153 Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/153 Installing : fedora-release-identity-basic-38-0.6.noarch 3/153 Installing : tzdata-2022g-1.fc38.noarch 4/153 Installing : rust-srpm-macros-23-1.fc38.noarch 5/153 Installing : qt5-srpm-macros-5.15.7-1.fc38.noarch 6/153 Installing : publicsuffix-list-dafsa-20221208-1.fc38.noarch 7/153 Installing : pkgconf-m4-1.8.0-3.fc37.noarch 8/153 Installing : perl-srpm-macros-1-47.fc38.noarch 9/153 Installing : pcre2-syntax-10.40-1.fc37.1.noarch 10/153 Installing : package-notes-srpm-macros-0.5-6.fc38.noarch 11/153 Installing : openblas-srpm-macros-2-12.fc37.noarch 12/153 Installing : ocaml-srpm-macros-7-2.fc37.noarch 13/153 Installing : nim-srpm-macros-3-7.fc37.noarch 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libtirpc-1.3.3-0.fc37.x86_64 92/153 Verifying : libunistring-1.0-2.fc37.x86_64 93/153 Verifying : libutempter-1.2.1-7.fc37.x86_64 94/153 Verifying : libuuid-2.38.1-3.fc38.x86_64 95/153 Verifying : libverto-0.3.2-4.fc37.x86_64 96/153 Verifying : libxcrypt-4.4.33-5.fc38.x86_64 97/153 Verifying : libxml2-2.10.3-2.fc38.x86_64 98/153 Verifying : libzstd-1.5.2-3.fc37.x86_64 99/153 Verifying : lua-libs-5.4.4-6.fc38.x86_64 100/153 Verifying : lua-srpm-macros-1-7.fc37.noarch 101/153 Verifying : lz4-libs-1.9.3-5.fc37.x86_64 102/153 Verifying : mpfr-4.1.1-2.fc38.x86_64 103/153 Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 104/153 Verifying : ncurses-libs-6.3-5.20221126.fc38.x86_64 105/153 Verifying : nettle-3.8-2.fc37.x86_64 106/153 Verifying : nim-srpm-macros-3-7.fc37.noarch 107/153 Verifying : ocaml-srpm-macros-7-2.fc37.noarch 108/153 Verifying : openblas-srpm-macros-2-12.fc37.noarch 109/153 Verifying : openldap-2.6.3-1.fc38.x86_64 110/153 Verifying : openssl-libs-1:3.0.5-6.fc38.x86_64 111/153 Verifying : p11-kit-0.24.1-5.fc38.x86_64 112/153 Verifying : p11-kit-trust-0.24.1-5.fc38.x86_64 113/153 Verifying : package-notes-srpm-macros-0.5-6.fc38.noarch 114/153 Verifying : pam-1.5.2-15.fc38.x86_64 115/153 Verifying : pam-libs-1.5.2-15.fc38.x86_64 116/153 Verifying : patch-2.7.6-17.fc37.x86_64 117/153 Verifying : pcre2-10.40-1.fc37.1.x86_64 118/153 Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 119/153 Verifying : perl-srpm-macros-1-47.fc38.noarch 120/153 Verifying : pkgconf-1.8.0-3.fc37.x86_64 121/153 Verifying : pkgconf-m4-1.8.0-3.fc37.noarch 122/153 Verifying : pkgconf-pkg-config-1.8.0-3.fc37.x86_64 123/153 Verifying : popt-1.19-1.fc38.x86_64 124/153 Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 125/153 Verifying : python-srpm-macros-3.11-6.fc38.noarch 126/153 Verifying : qt5-srpm-macros-5.15.7-1.fc38.noarch 127/153 Verifying : readline-8.2-2.fc38.x86_64 128/153 Verifying : redhat-rpm-config-235-1.fc38.noarch 129/153 Verifying : rpm-4.18.0-8.fc38.x86_64 130/153 Verifying : rpm-build-4.18.0-8.fc38.x86_64 131/153 Verifying : rpm-build-libs-4.18.0-8.fc38.x86_64 132/153 Verifying : rpm-libs-4.18.0-8.fc38.x86_64 133/153 Verifying : rpm-sequoia-1.2.0-1.fc38.x86_64 134/153 Verifying : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch 135/153 Verifying : rust-srpm-macros-23-1.fc38.noarch 136/153 Verifying : sed-4.8-11.fc37.x86_64 137/153 Verifying : setup-2.14.3-1.fc38.noarch 138/153 Verifying : shadow-utils-2:4.13-3.fc38.x86_64 139/153 Verifying : sqlite-libs-3.40.0-1.fc38.x86_64 140/153 Verifying : systemd-libs-252.4-598.fc38.x86_64 141/153 Verifying : tar-2:1.34-5.fc38.x86_64 142/153 Verifying : tzdata-2022g-1.fc38.noarch 143/153 Verifying : unzip-6.0-58.fc38.x86_64 144/153 Verifying : util-linux-2.38.1-3.fc38.x86_64 145/153 Verifying : util-linux-core-2.38.1-3.fc38.x86_64 146/153 Verifying : which-2.21-36.fc38.x86_64 147/153 Verifying : xxhash-libs-0.8.1-3.fc37.x86_64 148/153 Verifying : xz-5.2.9-1.fc38.x86_64 149/153 Verifying : xz-libs-5.2.9-1.fc38.x86_64 150/153 Verifying : zip-3.0-35.fc38.x86_64 151/153 Verifying : zlib-1.2.13-1.fc38.x86_64 152/153 Verifying : zstd-1.5.2-3.fc37.x86_64 153/153 Installed: alternatives-1.21-1.fc38.x86_64 ansible-srpm-macros-1-8.1.fc38.noarch audit-libs-3.0.9-1.fc38.x86_64 authselect-1.4.2-1.fc38.x86_64 authselect-libs-1.4.2-1.fc38.x86_64 basesystem-11-14.fc37.noarch bash-5.2.9-3.fc38.x86_64 binutils-2.39-6.fc38.x86_64 binutils-gold-2.39-6.fc38.x86_64 bzip2-1.0.8-12.fc37.x86_64 bzip2-libs-1.0.8-12.fc37.x86_64 ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-8.fc38.x86_64 coreutils-common-9.1-8.fc38.x86_64 cpio-2.13-13.fc38.x86_64 cracklib-2.9.7-30.fc38.x86_64 crypto-policies-20221215-1.gita4c31a3.fc38.noarch curl-7.87.0-1.fc38.x86_64 cyrus-sasl-lib-2.1.28-8.fc38.x86_64 debugedit-5.0-5.fc37.x86_64 diffutils-3.8-3.fc37.x86_64 dwz-0.15-1.fc38.x86_64 ed-1.18-2.fc37.x86_64 efi-srpm-macros-5-6.fc37.noarch elfutils-0.188-3.fc38.x86_64 elfutils-debuginfod-client-0.188-3.fc38.x86_64 elfutils-default-yama-scope-0.188-3.fc38.noarch elfutils-libelf-0.188-3.fc38.x86_64 elfutils-libs-0.188-3.fc38.x86_64 fedora-gpg-keys-38-0.3.noarch fedora-release-38-0.6.noarch fedora-release-common-38-0.6.noarch fedora-release-identity-basic-38-0.6.noarch fedora-repos-38-0.3.noarch fedora-repos-rawhide-38-0.3.noarch file-5.42-4.fc37.x86_64 file-libs-5.42-4.fc37.x86_64 filesystem-3.18-2.fc37.x86_64 findutils-1:4.9.0-2.fc37.x86_64 fonts-srpm-macros-1:2.0.5-10.fc38.noarch fpc-srpm-macros-1.3-6.fc37.noarch gawk-5.1.1-4.fc37.x86_64 gdb-minimal-12.1-10.fc38.x86_64 gdbm-libs-1:1.23-2.fc37.x86_64 ghc-srpm-macros-1.5.0-7.fc37.noarch glibc-2.36.9000-18.fc38.x86_64 glibc-common-2.36.9000-18.fc38.x86_64 glibc-gconv-extra-2.36.9000-18.fc38.x86_64 glibc-minimal-langpack-2.36.9000-18.fc38.x86_64 gmp-1:6.2.1-3.fc37.x86_64 gnat-srpm-macros-4-16.fc37.noarch go-srpm-macros-3.2.0-1.fc38.noarch grep-3.8-1.fc38.x86_64 gzip-1.12-2.fc37.x86_64 info-7.0.1-1.fc38.x86_64 jansson-2.13.1-5.fc37.x86_64 kernel-srpm-macros-1.0-15.fc37.noarch keyutils-libs-1.6.1-5.fc37.x86_64 krb5-libs-1.20.1-3.fc38.x86_64 libacl-2.3.1-4.fc38.x86_64 libarchive-3.6.1-3.fc38.x86_64 libattr-2.5.1-5.fc38.x86_64 libblkid-2.38.1-3.fc38.x86_64 libbrotli-1.0.9-9.fc37.x86_64 libcap-2.48-5.fc37.x86_64 libcap-ng-0.8.3-4.fc38.x86_64 libcom_err-1.46.5-3.fc37.x86_64 libcurl-7.87.0-1.fc38.x86_64 libdb-5.3.28-54.fc38.x86_64 libeconf-0.4.0-4.fc37.x86_64 libevent-2.1.12-7.fc37.x86_64 libfdisk-2.38.1-3.fc38.x86_64 libffi-3.4.4-1.fc38.x86_64 libgcc-13.0.0-0.4.fc38.x86_64 libgomp-13.0.0-0.4.fc38.x86_64 libidn2-2.3.4-1.fc38.x86_64 libmount-2.38.1-3.fc38.x86_64 libnghttp2-1.51.0-1.fc38.x86_64 libnsl2-2.0.0-4.fc37.x86_64 libpkgconf-1.8.0-3.fc37.x86_64 libpsl-0.21.1-6.fc37.x86_64 libpwquality-1.4.4-11.fc37.x86_64 libselinux-3.4-6.fc38.x86_64 libsemanage-3.4-6.fc38.x86_64 libsepol-3.4-4.fc38.x86_64 libsigsegv-2.14-3.fc37.x86_64 libsmartcols-2.38.1-3.fc38.x86_64 libssh-0.10.4-2.fc38.x86_64 libssh-config-0.10.4-2.fc38.noarch libstdc++-13.0.0-0.4.fc38.x86_64 libtasn1-4.19.0-1.fc38.x86_64 libtirpc-1.3.3-0.fc37.x86_64 libunistring-1.0-2.fc37.x86_64 libutempter-1.2.1-7.fc37.x86_64 libuuid-2.38.1-3.fc38.x86_64 libverto-0.3.2-4.fc37.x86_64 libxcrypt-4.4.33-5.fc38.x86_64 libxml2-2.10.3-2.fc38.x86_64 libzstd-1.5.2-3.fc37.x86_64 lua-libs-5.4.4-6.fc38.x86_64 lua-srpm-macros-1-7.fc37.noarch lz4-libs-1.9.3-5.fc37.x86_64 mpfr-4.1.1-2.fc38.x86_64 ncurses-base-6.3-5.20221126.fc38.noarch ncurses-libs-6.3-5.20221126.fc38.x86_64 nettle-3.8-2.fc37.x86_64 nim-srpm-macros-3-7.fc37.noarch ocaml-srpm-macros-7-2.fc37.noarch openblas-srpm-macros-2-12.fc37.noarch openldap-2.6.3-1.fc38.x86_64 openssl-libs-1:3.0.5-6.fc38.x86_64 p11-kit-0.24.1-5.fc38.x86_64 p11-kit-trust-0.24.1-5.fc38.x86_64 package-notes-srpm-macros-0.5-6.fc38.noarch pam-1.5.2-15.fc38.x86_64 pam-libs-1.5.2-15.fc38.x86_64 patch-2.7.6-17.fc37.x86_64 pcre2-10.40-1.fc37.1.x86_64 pcre2-syntax-10.40-1.fc37.1.noarch perl-srpm-macros-1-47.fc38.noarch pkgconf-1.8.0-3.fc37.x86_64 pkgconf-m4-1.8.0-3.fc37.noarch pkgconf-pkg-config-1.8.0-3.fc37.x86_64 popt-1.19-1.fc38.x86_64 publicsuffix-list-dafsa-20221208-1.fc38.noarch python-srpm-macros-3.11-6.fc38.noarch qt5-srpm-macros-5.15.7-1.fc38.noarch readline-8.2-2.fc38.x86_64 redhat-rpm-config-235-1.fc38.noarch rpm-4.18.0-8.fc38.x86_64 rpm-build-4.18.0-8.fc38.x86_64 rpm-build-libs-4.18.0-8.fc38.x86_64 rpm-libs-4.18.0-8.fc38.x86_64 rpm-sequoia-1.2.0-1.fc38.x86_64 rpmautospec-rpm-macros-0.3.1-1.fc38.noarch rust-srpm-macros-23-1.fc38.noarch sed-4.8-11.fc37.x86_64 setup-2.14.3-1.fc38.noarch shadow-utils-2:4.13-3.fc38.x86_64 sqlite-libs-3.40.0-1.fc38.x86_64 systemd-libs-252.4-598.fc38.x86_64 tar-2:1.34-5.fc38.x86_64 tzdata-2022g-1.fc38.noarch unzip-6.0-58.fc38.x86_64 util-linux-2.38.1-3.fc38.x86_64 util-linux-core-2.38.1-3.fc38.x86_64 which-2.21-36.fc38.x86_64 xxhash-libs-0.8.1-3.fc37.x86_64 xz-5.2.9-1.fc38.x86_64 xz-libs-5.2.9-1.fc38.x86_64 zip-3.0-35.fc38.x86_64 zlib-1.2.13-1.fc38.x86_64 zstd-1.5.2-3.fc37.x86_64 Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: fpc-srpm-macros-1.3-6.fc37.noarch gnat-srpm-macros-4-16.fc37.noarch openblas-srpm-macros-2-12.fc37.noarch cyrus-sasl-lib-2.1.28-8.fc38.x86_64 bzip2-libs-1.0.8-12.fc37.x86_64 audit-libs-3.0.9-1.fc38.x86_64 lua-libs-5.4.4-6.fc38.x86_64 python-srpm-macros-3.11-6.fc38.noarch publicsuffix-list-dafsa-20221208-1.fc38.noarch glibc-2.36.9000-18.fc38.x86_64 lz4-libs-1.9.3-5.fc37.x86_64 pcre2-syntax-10.40-1.fc37.1.noarch perl-srpm-macros-1-47.fc38.noarch cracklib-2.9.7-30.fc38.x86_64 libgomp-13.0.0-0.4.fc38.x86_64 libidn2-2.3.4-1.fc38.x86_64 libutempter-1.2.1-7.fc37.x86_64 util-linux-core-2.38.1-3.fc38.x86_64 patch-2.7.6-17.fc37.x86_64 libuuid-2.38.1-3.fc38.x86_64 libcom_err-1.46.5-3.fc37.x86_64 libarchive-3.6.1-3.fc38.x86_64 coreutils-common-9.1-8.fc38.x86_64 ghc-srpm-macros-1.5.0-7.fc37.noarch p11-kit-trust-0.24.1-5.fc38.x86_64 qt5-srpm-macros-5.15.7-1.fc38.noarch gdbm-libs-1.23-2.fc37.x86_64 nim-srpm-macros-3-7.fc37.noarch binutils-2.39-6.fc38.x86_64 libgcc-13.0.0-0.4.fc38.x86_64 alternatives-1.21-1.fc38.x86_64 libpkgconf-1.8.0-3.fc37.x86_64 authselect-1.4.2-1.fc38.x86_64 ocaml-srpm-macros-7-2.fc37.noarch zlib-1.2.13-1.fc38.x86_64 openldap-2.6.3-1.fc38.x86_64 ncurses-libs-6.3-5.20221126.fc38.x86_64 libeconf-0.4.0-4.fc37.x86_64 crypto-policies-20221215-1.gita4c31a3.fc38.noarch glibc-gconv-extra-2.36.9000-18.fc38.x86_64 fedora-repos-38-0.3.noarch xz-libs-5.2.9-1.fc38.x86_64 ansible-srpm-macros-1-8.1.fc38.noarch libpwquality-1.4.4-11.fc37.x86_64 redhat-rpm-config-235-1.fc38.noarch rpm-build-libs-4.18.0-8.fc38.x86_64 rpmautospec-rpm-macros-0.3.1-1.fc38.noarch gmp-6.2.1-3.fc37.x86_64 mpfr-4.1.1-2.fc38.x86_64 glibc-minimal-langpack-2.36.9000-18.fc38.x86_64 libffi-3.4.4-1.fc38.x86_64 dwz-0.15-1.fc38.x86_64 efi-srpm-macros-5-6.fc37.noarch gpg-pubkey-eb10b464-6202d9c6 util-linux-2.38.1-3.fc38.x86_64 libnghttp2-1.51.0-1.fc38.x86_64 gzip-1.12-2.fc37.x86_64 coreutils-9.1-8.fc38.x86_64 libssh-config-0.10.4-2.fc38.noarch ca-certificates-2022.2.54-5.fc37.noarch elfutils-libs-0.188-3.fc38.x86_64 systemd-libs-252.4-598.fc38.x86_64 diffutils-3.8-3.fc37.x86_64 libselinux-3.4-6.fc38.x86_64 cpio-2.13-13.fc38.x86_64 libsepol-3.4-4.fc38.x86_64 jansson-2.13.1-5.fc37.x86_64 keyutils-libs-1.6.1-5.fc37.x86_64 libattr-2.5.1-5.fc38.x86_64 libstdc++-13.0.0-0.4.fc38.x86_64 package-notes-srpm-macros-0.5-6.fc38.noarch grep-3.8-1.fc38.x86_64 libxml2-2.10.3-2.fc38.x86_64 tzdata-2022g-1.fc38.noarch libsmartcols-2.38.1-3.fc38.x86_64 pkgconf-pkg-config-1.8.0-3.fc37.x86_64 filesystem-3.18-2.fc37.x86_64 rpm-libs-4.18.0-8.fc38.x86_64 libssh-0.10.4-2.fc38.x86_64 sed-4.8-11.fc37.x86_64 bzip2-1.0.8-12.fc37.x86_64 pam-1.5.2-15.fc38.x86_64 rpm-build-4.18.0-8.fc38.x86_64 libverto-0.3.2-4.fc37.x86_64 libcurl-7.87.0-1.fc38.x86_64 xxhash-libs-0.8.1-3.fc37.x86_64 fedora-release-identity-basic-38-0.6.noarch zstd-1.5.2-3.fc37.x86_64 elfutils-0.188-3.fc38.x86_64 p11-kit-0.24.1-5.fc38.x86_64 gawk-5.1.1-4.fc37.x86_64 gpg-pubkey-5323552a-6112bcdc libcap-ng-0.8.3-4.fc38.x86_64 pcre2-10.40-1.fc37.1.x86_64 libtasn1-4.19.0-1.fc38.x86_64 fedora-repos-rawhide-38-0.3.noarch file-5.42-4.fc37.x86_64 curl-7.87.0-1.fc38.x86_64 libzstd-1.5.2-3.fc37.x86_64 sqlite-libs-3.40.0-1.fc38.x86_64 libmount-2.38.1-3.fc38.x86_64 ncurses-base-6.3-5.20221126.fc38.noarch kernel-srpm-macros-1.0-15.fc37.noarch libblkid-2.38.1-3.fc38.x86_64 file-libs-5.42-4.fc37.x86_64 elfutils-libelf-0.188-3.fc38.x86_64 elfutils-debuginfod-client-0.188-3.fc38.x86_64 binutils-gold-2.39-6.fc38.x86_64 setup-2.14.3-1.fc38.noarch libcap-2.48-5.fc37.x86_64 fedora-release-common-38-0.6.noarch popt-1.19-1.fc38.x86_64 libtirpc-1.3.3-0.fc37.x86_64 libevent-2.1.12-7.fc37.x86_64 authselect-libs-1.4.2-1.fc38.x86_64 rpm-sequoia-1.2.0-1.fc38.x86_64 gdb-minimal-12.1-10.fc38.x86_64 libsigsegv-2.14-3.fc37.x86_64 fedora-gpg-keys-38-0.3.noarch pkgconf-m4-1.8.0-3.fc37.noarch libpsl-0.21.1-6.fc37.x86_64 info-7.0.1-1.fc38.x86_64 libacl-2.3.1-4.fc38.x86_64 elfutils-default-yama-scope-0.188-3.fc38.noarch findutils-4.9.0-2.fc37.x86_64 rust-srpm-macros-23-1.fc38.noarch krb5-libs-1.20.1-3.fc38.x86_64 ed-1.18-2.fc37.x86_64 xz-5.2.9-1.fc38.x86_64 which-2.21-36.fc38.x86_64 fedora-release-38-0.6.noarch nettle-3.8-2.fc37.x86_64 rpm-4.18.0-8.fc38.x86_64 libxcrypt-4.4.33-5.fc38.x86_64 libnsl2-2.0.0-4.fc37.x86_64 bash-5.2.9-3.fc38.x86_64 readline-8.2-2.fc38.x86_64 openssl-libs-3.0.5-6.fc38.x86_64 libbrotli-1.0.9-9.fc37.x86_64 basesystem-11-14.fc37.noarch libfdisk-2.38.1-3.fc38.x86_64 zip-3.0-35.fc38.x86_64 lua-srpm-macros-1-7.fc37.noarch libsemanage-3.4-6.fc38.x86_64 fonts-srpm-macros-2.0.5-10.fc38.noarch tar-1.34-5.fc38.x86_64 libdb-5.3.28-54.fc38.x86_64 go-srpm-macros-3.2.0-1.fc38.noarch pam-libs-1.5.2-15.fc38.x86_64 pkgconf-1.8.0-3.fc37.x86_64 glibc-common-2.36.9000-18.fc38.x86_64 shadow-utils-4.13-3.fc38.x86_64 debugedit-5.0-5.fc37.x86_64 unzip-6.0-58.fc38.x86_64 libunistring-1.0-2.fc37.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1661212800 Wrote: /builddir/build/SRPMS/bcftools-1.15.1-2.fc38.src.rpm Finish: rpmbuild -bs cp: ‘var/lib/mock/fedora-rawhide-x86_64-1671795578.114598/root/var/log’: No such file or directory INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1671795578.114598/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1671795578.114598/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1671795578.114598/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-xqei4s3q/bcftools/bcftools.spec) Config(child) 0 minutes 48 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 (timeout=115200): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/bcftools-1.15.1-2.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1671795578.114598 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)... 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/results/bcftools-1.15.1-2.fc38.src.rpm) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1671795578.114598/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1671795578.114598/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: enabled HW Info plugin Mock Version: 3.5 INFO: Mock Version: 3.5 Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1671795578.114598/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 Mock Version: 3.5 INFO: Mock Version: 3.5 Start: dnf update No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 13 kB/s | 3.0 kB 00:00 Additional repo https_jakub_fedorapeople_org_fe 12 kB/s | 3.0 kB 00:00 fedora 86 kB/s | 23 kB 00:00 Dependencies resolved. Nothing to do. Complete! Finish: dnf update Finish: chroot init Start: build phase for bcftools-1.15.1-2.fc38.src.rpm Start: build setup for bcftools-1.15.1-2.fc38.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1661212800 Wrote: /builddir/build/SRPMS/bcftools-1.15.1-2.fc38.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 13 kB/s | 3.0 kB 00:00 Additional repo https_jakub_fedorapeople_org_fe 11 kB/s | 3.0 kB 00:00 fedora 99 kB/s | 23 kB 00:00 Dependencies resolved. ======================================================================================================================== Package Arch Version Repository Size ======================================================================================================================== Installing: gcc x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 34 M gsl-devel x86_64 2.7.1-2.fc38 fedora 653 k htslib-devel x86_64 1.15.1-1.fc38 fedora 105 k htslib-tools x86_64 1.15.1-1.fc38 fedora 533 k make x86_64 1:4.3-11.fc37 fedora 542 k perl-ExtUtils-Embed noarch 1.35-492.fc38 fedora 21 k perl-File-Temp noarch 1:0.231.100-489.fc37 fedora 59 k perl-FindBin noarch 1.53-492.fc38 fedora 17 k perl-Getopt-Long noarch 1:2.54-1.fc38 fedora 60 k perl-interpreter x86_64 4:5.36.0-492.fc38 fedora 75 k zlib-devel x86_64 1.2.13-1.fc38 fedora 45 k Installing dependencies: annobin-docs noarch 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 93 k annobin-plugin-gcc x86_64 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 889 k autoconf noarch 2.71-4.fc38 copr_base 720 k automake noarch 1.16.5-9.fc37 fedora 696 k cpp x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 11 M emacs-filesystem noarch 1:28.1-3.fc37 fedora 9.5 k expat x86_64 2.5.0-1.fc38 fedora 110 k gc x86_64 8.2.2-1.fc38 fedora 110 k gcc-plugin-annobin x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 29 k glibc-devel x86_64 2.36.9000-18.fc38 fedora 47 k glibc-headers-x86 noarch 2.36.9000-18.fc38 fedora 525 k groff-base x86_64 1.22.4-10.fc37 fedora 1.1 M gsl x86_64 2.7.1-2.fc38 fedora 1.1 M guile22 x86_64 2.2.7-6.fc37 fedora 6.5 M htslib x86_64 1.15.1-1.fc38 fedora 487 k kernel-headers x86_64 6.1.0-1.fc38 fedora 1.5 M libb2 x86_64 0.98.1-7.fc37 fedora 25 k libmpc x86_64 1.2.1-5.fc37 fedora 61 k libtool-ltdl x86_64 2.4.7-3.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 37 k libxcrypt-devel x86_64 4.4.33-5.fc38 fedora 30 k m4 x86_64 1.4.19-4.fc37 fedora 303 k mpdecimal x86_64 2.5.1-4.fc37 fedora 102 k ncurses x86_64 6.3-5.20221126.fc38 fedora 412 k perl-AutoSplit noarch 5.74-492.fc38 fedora 25 k perl-B x86_64 1.83-492.fc38 fedora 184 k perl-Benchmark noarch 1.23-492.fc38 fedora 30 k perl-Carp noarch 1.52-489.fc37 fedora 29 k perl-Class-Struct noarch 0.66-492.fc38 fedora 25 k perl-Data-Dumper x86_64 2.184-490.fc37 fedora 56 k perl-Devel-PPPort x86_64 3.68-490.fc37 fedora 218 k perl-DynaLoader x86_64 1.52-492.fc38 fedora 29 k perl-Encode x86_64 4:3.19-492.fc38 fedora 1.7 M perl-Errno x86_64 1.36-492.fc38 fedora 18 k perl-Exporter noarch 5.77-489.fc37 fedora 31 k perl-ExtUtils-Command noarch 2:7.64-490.fc37 fedora 14 k perl-ExtUtils-Constant noarch 0.25-492.fc38 fedora 50 k perl-ExtUtils-Install noarch 2.20-489.fc37 fedora 44 k perl-ExtUtils-MakeMaker noarch 2:7.64-490.fc37 fedora 301 k perl-ExtUtils-Manifest noarch 1:1.73-489.fc37 fedora 34 k perl-ExtUtils-ParseXS noarch 1:3.45-489.fc37 fedora 188 k perl-Fcntl x86_64 1.15-492.fc38 fedora 24 k perl-File-Basename noarch 2.85-492.fc38 fedora 20 k perl-File-Compare noarch 1.100.700-492.fc38 fedora 16 k perl-File-Copy noarch 2.39-492.fc38 fedora 23 k perl-File-Find noarch 1.40-492.fc38 fedora 28 k perl-File-Path noarch 2.18-489.fc37 fedora 35 k perl-File-stat noarch 1.12-492.fc38 fedora 20 k perl-Getopt-Std noarch 1.13-492.fc38 fedora 19 k perl-HTTP-Tiny noarch 0.082-1.fc37 fedora 55 k perl-IO x86_64 1.50-492.fc38 fedora 95 k perl-IPC-Open3 noarch 1.22-492.fc38 fedora 26 k perl-MIME-Base64 x86_64 3.16-489.fc37 fedora 30 k perl-POSIX x86_64 2.03-492.fc38 fedora 101 k perl-PathTools x86_64 3.84-489.fc37 fedora 89 k perl-Pod-Escapes noarch 1:1.07-489.fc37 fedora 20 k perl-Pod-Perldoc noarch 3.28.01-490.fc37 fedora 90 k perl-Pod-Simple noarch 1:3.43-490.fc37 fedora 225 k perl-Pod-Usage noarch 4:2.03-3.fc37 fedora 40 k perl-Scalar-List-Utils x86_64 5:1.63-489.fc38 fedora 72 k perl-SelectSaver noarch 1.02-492.fc38 fedora 15 k perl-Socket x86_64 4:2.036-1.fc38 fedora 55 k perl-Storable x86_64 1:3.26-489.fc37 fedora 97 k perl-Symbol noarch 1.09-492.fc38 fedora 17 k perl-Term-ANSIColor noarch 5.01-490.fc37 fedora 48 k perl-Term-Cap noarch 1.17-489.fc37 fedora 22 k perl-Test-Harness noarch 1:3.44-490.fc37 fedora 288 k perl-Text-ParseWords noarch 3.31-489.fc37 fedora 16 k perl-Text-Tabs+Wrap noarch 2021.0814-489.fc37 fedora 22 k perl-Thread-Queue noarch 3.14-489.fc37 fedora 21 k perl-Time-Local noarch 2:1.300-489.fc37 fedora 33 k perl-base noarch 2.27-492.fc38 fedora 19 k perl-constant noarch 1.33-490.fc37 fedora 23 k perl-devel x86_64 4:5.36.0-492.fc38 fedora 714 k perl-if noarch 0.61.000-492.fc38 fedora 17 k perl-lib x86_64 0.65-492.fc38 fedora 18 k perl-libs x86_64 4:5.36.0-492.fc38 fedora 2.2 M perl-locale noarch 1.10-492.fc38 fedora 17 k perl-mro x86_64 1.26-492.fc38 fedora 32 k perl-overload noarch 1.35-492.fc38 fedora 49 k perl-overloading noarch 0.02-492.fc38 fedora 16 k perl-parent noarch 1:0.239-1.fc38 fedora 14 k perl-podlators noarch 1:5.00-1.fc38 fedora 127 k perl-threads x86_64 1:2.27-489.fc37 fedora 57 k perl-threads-shared x86_64 1.64-489.fc37 fedora 44 k perl-vars noarch 1.05-492.fc38 fedora 16 k perl-version x86_64 8:0.99.29-490.fc37 fedora 63 k python-pip-wheel noarch 22.3.1-1.fc38 fedora 1.4 M python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k python3 x86_64 3.11.1-1.fc38 fedora 27 k python3-libs x86_64 3.11.1-1.fc38 fedora 9.6 M python3-pyparsing noarch 3.0.9-2.fc37 fedora 262 k systemtap-sdt-devel x86_64 4.8~pre16650659g6a096a7d-1.fc38 fedora 73 k Transaction Summary ======================================================================================================================== Install 103 Packages Total size: 81 M Total download size: 5.2 M Installed size: 278 M Downloading Packages: [SKIPPED] autoconf-2.71-4.fc38.noarch.rpm: Already downloaded [SKIPPED] annobin-docs-10.99-1.0.1.fc38.noarch.rpm: Already downloaded [SKIPPED] annobin-plugin-gcc-10.99-1.0.1.fc38.x86_64.rpm: Already downloaded [SKIPPED] cpp-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded [SKIPPED] gcc-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded [SKIPPED] gcc-plugin-annobin-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libtool-ltdl-2.4.7-3.0.1.fc38.x86_64.rpm: Already downloaded [SKIPPED] automake-1.16.5-9.fc37.noarch.rpm: Already downloaded [SKIPPED] emacs-filesystem-28.1-3.fc37.noarch.rpm: Already downloaded [SKIPPED] expat-2.5.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] gc-8.2.2-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-devel-2.36.9000-18.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-headers-x86-2.36.9000-18.fc38.noarch.rpm: Already downloaded [SKIPPED] groff-base-1.22.4-10.fc37.x86_64.rpm: Already downloaded [SKIPPED] guile22-2.2.7-6.fc37.x86_64.rpm: Already downloaded [SKIPPED] kernel-headers-6.1.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libb2-0.98.1-7.fc37.x86_64.rpm: Already downloaded [SKIPPED] libmpc-1.2.1-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] libxcrypt-devel-4.4.33-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] m4-1.4.19-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] make-4.3-11.fc37.x86_64.rpm: Already downloaded [SKIPPED] mpdecimal-2.5.1-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] ncurses-6.3-5.20221126.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-B-1.83-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-Carp-1.52-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Class-Struct-0.66-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-Data-Dumper-2.184-490.fc37.x86_64.rpm: Already downloaded [SKIPPED] perl-DynaLoader-1.52-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-Encode-3.19-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-Errno-1.36-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-Exporter-5.77-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Fcntl-1.15-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-File-Basename-2.85-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-File-Compare-1.100.700-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-File-Copy-2.39-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-File-Find-1.40-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-File-Path-2.18-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-File-Temp-0.231.100-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-File-stat-1.12-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-Getopt-Long-2.54-1.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-Getopt-Std-1.13-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-HTTP-Tiny-0.082-1.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-IO-1.50-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-IPC-Open3-1.22-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-MIME-Base64-3.16-489.fc37.x86_64.rpm: Already downloaded [SKIPPED] perl-POSIX-2.03-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-PathTools-3.84-489.fc37.x86_64.rpm: Already downloaded [SKIPPED] perl-Pod-Escapes-1.07-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Pod-Perldoc-3.28.01-490.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Pod-Simple-3.43-490.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Pod-Usage-2.03-3.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Scalar-List-Utils-1.63-489.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-SelectSaver-1.02-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-Socket-2.036-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-Storable-3.26-489.fc37.x86_64.rpm: Already downloaded [SKIPPED] perl-Symbol-1.09-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-Term-ANSIColor-5.01-490.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Term-Cap-1.17-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Text-ParseWords-3.31-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Thread-Queue-3.14-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Time-Local-1.300-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-constant-1.33-490.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-if-0.61.000-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-interpreter-5.36.0-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-libs-5.36.0-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-mro-1.26-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-overload-1.35-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-overloading-0.02-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-parent-0.239-1.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-podlators-5.00-1.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-threads-2.27-489.fc37.x86_64.rpm: Already downloaded [SKIPPED] perl-threads-shared-1.64-489.fc37.x86_64.rpm: Already downloaded [SKIPPED] perl-vars-1.05-492.fc38.noarch.rpm: Already downloaded [SKIPPED] python-pip-wheel-22.3.1-1.fc38.noarch.rpm: Already downloaded [SKIPPED] python-setuptools-wheel-65.5.1-1.fc38.noarch.rpm: Already downloaded [SKIPPED] python3-3.11.1-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] python3-libs-3.11.1-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] zlib-devel-1.2.13-1.fc38.x86_64.rpm: Already downloaded (80/103): gsl-devel-2.7.1-2.fc38.x86_64.rpm 797 kB/s | 653 kB 00:00 (81/103): gsl-2.7.1-2.fc38.x86_64.rpm 1.3 MB/s | 1.1 MB 00:00 (82/103): htslib-1.15.1-1.fc38.x86_64.rpm 550 kB/s | 487 kB 00:00 (83/103): htslib-devel-1.15.1-1.fc38.x86_64.rpm 967 kB/s | 105 kB 00:00 (84/103): htslib-tools-1.15.1-1.fc38.x86_64.rpm 2.3 MB/s | 533 kB 00:00 (85/103): perl-AutoSplit-5.74-492.fc38.noarch.r 122 kB/s | 25 kB 00:00 (86/103): perl-Benchmark-1.23-492.fc38.noarch.r 189 kB/s | 30 kB 00:00 (87/103): perl-Devel-PPPort-3.68-490.fc37.x86_6 1.3 MB/s | 218 kB 00:00 (88/103): perl-ExtUtils-Command-7.64-490.fc37.n 81 kB/s | 14 kB 00:00 (89/103): perl-ExtUtils-Constant-0.25-492.fc38. 237 kB/s | 50 kB 00:00 (90/103): perl-ExtUtils-Embed-1.35-492.fc38.noa 326 kB/s | 21 kB 00:00 (91/103): perl-ExtUtils-Install-2.20-489.fc37.n 700 kB/s | 44 kB 00:00 (92/103): perl-ExtUtils-MakeMaker-7.64-490.fc37 2.7 MB/s | 301 kB 00:00 (93/103): perl-ExtUtils-Manifest-1.73-489.fc37. 223 kB/s | 34 kB 00:00 (94/103): perl-ExtUtils-ParseXS-3.45-489.fc37.n 1.1 MB/s | 188 kB 00:00 (95/103): perl-FindBin-1.53-492.fc38.noarch.rpm 172 kB/s | 17 kB 00:00 (96/103): perl-Test-Harness-3.44-490.fc37.noarc 2.9 MB/s | 288 kB 00:00 (97/103): perl-base-2.27-492.fc38.noarch.rpm 240 kB/s | 19 kB 00:00 (98/103): perl-devel-5.36.0-492.fc38.x86_64.rpm 5.1 MB/s | 714 kB 00:00 (99/103): perl-lib-0.65-492.fc38.x86_64.rpm 184 kB/s | 18 kB 00:00 (100/103): perl-locale-1.10-492.fc38.noarch.rpm 142 kB/s | 17 kB 00:00 (101/103): perl-version-0.99.29-490.fc37.x86_64 979 kB/s | 63 kB 00:00 (102/103): python3-pyparsing-3.0.9-2.fc37.noarc 3.5 MB/s | 262 kB 00:00 (103/103): systemtap-sdt-devel-4.8~pre16650659g 885 kB/s | 73 kB 00:00 -------------------------------------------------------------------------------- Total 2.4 MB/s | 5.2 MB 00:02 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.2.1-5.fc37.x86_64 1/103 Installing : htslib-1.15.1-1.fc38.x86_64 2/103 Installing : cpp-13.0.0-0.4.fc38.x86_64 3/103 Installing : python-setuptools-wheel-65.5.1-1.fc38.noarch 4/103 Installing : python-pip-wheel-22.3.1-1.fc38.noarch 5/103 Installing : ncurses-6.3-5.20221126.fc38.x86_64 6/103 Installing : mpdecimal-2.5.1-4.fc37.x86_64 7/103 Installing : m4-1.4.19-4.fc37.x86_64 8/103 Installing : libb2-0.98.1-7.fc37.x86_64 9/103 Installing : kernel-headers-6.1.0-1.fc38.x86_64 10/103 Installing : gsl-2.7.1-2.fc38.x86_64 11/103 Running scriptlet: groff-base-1.22.4-10.fc37.x86_64 12/103 Installing : groff-base-1.22.4-10.fc37.x86_64 12/103 Running scriptlet: groff-base-1.22.4-10.fc37.x86_64 12/103 Installing : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 13/103 Installing : perl-if-0.61.000-492.fc38.noarch 14/103 Installing : perl-Time-Local-2:1.300-489.fc37.noarch 15/103 Installing : perl-File-Path-2.18-489.fc37.noarch 16/103 Installing : perl-Pod-Escapes-1:1.07-489.fc37.noarch 17/103 Installing : perl-Class-Struct-0.66-492.fc38.noarch 18/103 Installing : perl-POSIX-2.03-492.fc38.x86_64 19/103 Installing : perl-Term-ANSIColor-5.01-490.fc37.noarch 20/103 Installing : perl-IPC-Open3-1.22-492.fc38.noarch 21/103 Installing : perl-HTTP-Tiny-0.082-1.fc37.noarch 22/103 Installing : perl-File-Temp-1:0.231.100-489.fc37.noarch 23/103 Installing : perl-Term-Cap-1.17-489.fc37.noarch 24/103 Installing : perl-Pod-Simple-1:3.43-490.fc37.noarch 25/103 Installing : perl-Socket-4:2.036-1.fc38.x86_64 26/103 Installing : perl-SelectSaver-1.02-492.fc38.noarch 27/103 Installing : perl-Symbol-1.09-492.fc38.noarch 28/103 Installing : perl-File-stat-1.12-492.fc38.noarch 29/103 Installing : perl-podlators-1:5.00-1.fc38.noarch 30/103 Installing : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 31/103 Installing : perl-Fcntl-1.15-492.fc38.x86_64 32/103 Installing : perl-Text-ParseWords-3.31-489.fc37.noarch 33/103 Installing : perl-mro-1.26-492.fc38.x86_64 34/103 Installing : perl-IO-1.50-492.fc38.x86_64 35/103 Installing : perl-overloading-0.02-492.fc38.noarch 36/103 Installing : perl-Pod-Usage-4:2.03-3.fc37.noarch 37/103 Installing : perl-Errno-1.36-492.fc38.x86_64 38/103 Installing : perl-File-Basename-2.85-492.fc38.noarch 39/103 Installing : perl-Getopt-Std-1.13-492.fc38.noarch 40/103 Installing : perl-MIME-Base64-3.16-489.fc37.x86_64 41/103 Installing : perl-Scalar-List-Utils-5:1.63-489.fc38.x86_64 42/103 Installing : perl-constant-1.33-490.fc37.noarch 43/103 Installing : perl-Storable-1:3.26-489.fc37.x86_64 44/103 Installing : perl-overload-1.35-492.fc38.noarch 45/103 Installing : perl-parent-1:0.239-1.fc38.noarch 46/103 Installing : perl-vars-1.05-492.fc38.noarch 47/103 Installing : perl-Getopt-Long-1:2.54-1.fc38.noarch 48/103 Installing : perl-Carp-1.52-489.fc37.noarch 49/103 Installing : perl-Exporter-5.77-489.fc37.noarch 50/103 Installing : perl-PathTools-3.84-489.fc37.x86_64 51/103 Installing : perl-DynaLoader-1.52-492.fc38.x86_64 52/103 Installing : perl-Encode-4:3.19-492.fc38.x86_64 53/103 Installing : perl-libs-4:5.36.0-492.fc38.x86_64 54/103 Installing : perl-interpreter-4:5.36.0-492.fc38.x86_64 55/103 Installing : perl-File-Find-1.40-492.fc38.noarch 56/103 Installing : perl-File-Copy-2.39-492.fc38.noarch 57/103 Installing : perl-Data-Dumper-2.184-490.fc37.x86_64 58/103 Installing : perl-B-1.83-492.fc38.x86_64 59/103 Installing : perl-File-Compare-1.100.700-492.fc38.noarch 60/103 Installing : perl-ExtUtils-ParseXS-1:3.45-489.fc37.noarch 61/103 Installing : perl-threads-1:2.27-489.fc37.x86_64 62/103 Installing : perl-threads-shared-1.64-489.fc37.x86_64 63/103 Installing : perl-Thread-Queue-3.14-489.fc37.noarch 64/103 Installing : perl-ExtUtils-Constant-0.25-492.fc38.noarch 65/103 Installing : perl-ExtUtils-Command-2:7.64-490.fc37.noarch 66/103 Installing : perl-ExtUtils-Manifest-1:1.73-489.fc37.noarch 67/103 Installing : perl-AutoSplit-5.74-492.fc38.noarch 68/103 Installing : perl-Benchmark-1.23-492.fc38.noarch 69/103 Installing : perl-Devel-PPPort-3.68-490.fc37.x86_64 70/103 Installing : perl-base-2.27-492.fc38.noarch 71/103 Installing : perl-Test-Harness-1:3.44-490.fc37.noarch 72/103 Installing : perl-lib-0.65-492.fc38.x86_64 73/103 Installing : perl-locale-1.10-492.fc38.noarch 74/103 Installing : perl-version-8:0.99.29-490.fc37.x86_64 75/103 Installing : glibc-headers-x86-2.36.9000-18.fc38.noarch 76/103 Installing : libxcrypt-devel-4.4.33-5.fc38.x86_64 77/103 Installing : glibc-devel-2.36.9000-18.fc38.x86_64 78/103 Installing : gc-8.2.2-1.fc38.x86_64 79/103 Installing : expat-2.5.0-1.fc38.x86_64 80/103 Installing : python3-3.11.1-1.fc38.x86_64 81/103 Installing : python3-libs-3.11.1-1.fc38.x86_64 82/103 Installing : python3-pyparsing-3.0.9-2.fc37.noarch 83/103 Installing : systemtap-sdt-devel-4.8~pre16650659g6a096a7d-1.f 84/103 Installing : emacs-filesystem-1:28.1-3.fc37.noarch 85/103 Installing : autoconf-2.71-4.fc38.noarch 86/103 Installing : automake-1.16.5-9.fc37.noarch 87/103 Installing : libtool-ltdl-2.4.7-3.0.1.fc38.x86_64 88/103 Installing : guile22-2.2.7-6.fc37.x86_64 89/103 Installing : make-1:4.3-11.fc37.x86_64 90/103 Installing : gcc-13.0.0-0.4.fc38.x86_64 91/103 Running scriptlet: gcc-13.0.0-0.4.fc38.x86_64 91/103 Installing : perl-devel-4:5.36.0-492.fc38.x86_64 92/103 Installing : perl-ExtUtils-Install-2.20-489.fc37.noarch 93/103 Installing : perl-ExtUtils-MakeMaker-2:7.64-490.fc37.noarch 94/103 Installing : annobin-docs-10.99-1.0.1.fc38.noarch 95/103 Installing : annobin-plugin-gcc-10.99-1.0.1.fc38.x86_64 96/103 Running scriptlet: annobin-plugin-gcc-10.99-1.0.1.fc38.x86_64 96/103 Installing : perl-ExtUtils-Embed-1.35-492.fc38.noarch 97/103 Installing : gcc-plugin-annobin-13.0.0-0.4.fc38.x86_64 98/103 Installing : gsl-devel-2.7.1-2.fc38.x86_64 99/103 Installing : perl-FindBin-1.53-492.fc38.noarch 100/103 Installing : htslib-devel-1.15.1-1.fc38.x86_64 101/103 Installing : htslib-tools-1.15.1-1.fc38.x86_64 102/103 Installing : zlib-devel-1.2.13-1.fc38.x86_64 103/103 Running scriptlet: zlib-devel-1.2.13-1.fc38.x86_64 103/103 Verifying : autoconf-2.71-4.fc38.noarch 1/103 Verifying : annobin-docs-10.99-1.0.1.fc38.noarch 2/103 Verifying : annobin-plugin-gcc-10.99-1.0.1.fc38.x86_64 3/103 Verifying : cpp-13.0.0-0.4.fc38.x86_64 4/103 Verifying : gcc-13.0.0-0.4.fc38.x86_64 5/103 Verifying : gcc-plugin-annobin-13.0.0-0.4.fc38.x86_64 6/103 Verifying : libtool-ltdl-2.4.7-3.0.1.fc38.x86_64 7/103 Verifying : automake-1.16.5-9.fc37.noarch 8/103 Verifying : emacs-filesystem-1:28.1-3.fc37.noarch 9/103 Verifying : expat-2.5.0-1.fc38.x86_64 10/103 Verifying : gc-8.2.2-1.fc38.x86_64 11/103 Verifying : glibc-devel-2.36.9000-18.fc38.x86_64 12/103 Verifying : glibc-headers-x86-2.36.9000-18.fc38.noarch 13/103 Verifying : groff-base-1.22.4-10.fc37.x86_64 14/103 Verifying : gsl-2.7.1-2.fc38.x86_64 15/103 Verifying : gsl-devel-2.7.1-2.fc38.x86_64 16/103 Verifying : guile22-2.2.7-6.fc37.x86_64 17/103 Verifying : htslib-1.15.1-1.fc38.x86_64 18/103 Verifying : htslib-devel-1.15.1-1.fc38.x86_64 19/103 Verifying : htslib-tools-1.15.1-1.fc38.x86_64 20/103 Verifying : kernel-headers-6.1.0-1.fc38.x86_64 21/103 Verifying : libb2-0.98.1-7.fc37.x86_64 22/103 Verifying : libmpc-1.2.1-5.fc37.x86_64 23/103 Verifying : libxcrypt-devel-4.4.33-5.fc38.x86_64 24/103 Verifying : m4-1.4.19-4.fc37.x86_64 25/103 Verifying : make-1:4.3-11.fc37.x86_64 26/103 Verifying : mpdecimal-2.5.1-4.fc37.x86_64 27/103 Verifying : ncurses-6.3-5.20221126.fc38.x86_64 28/103 Verifying : perl-AutoSplit-5.74-492.fc38.noarch 29/103 Verifying : perl-B-1.83-492.fc38.x86_64 30/103 Verifying : perl-Benchmark-1.23-492.fc38.noarch 31/103 Verifying : perl-Carp-1.52-489.fc37.noarch 32/103 Verifying : perl-Class-Struct-0.66-492.fc38.noarch 33/103 Verifying : perl-Data-Dumper-2.184-490.fc37.x86_64 34/103 Verifying : perl-Devel-PPPort-3.68-490.fc37.x86_64 35/103 Verifying : perl-DynaLoader-1.52-492.fc38.x86_64 36/103 Verifying : perl-Encode-4:3.19-492.fc38.x86_64 37/103 Verifying : perl-Errno-1.36-492.fc38.x86_64 38/103 Verifying : perl-Exporter-5.77-489.fc37.noarch 39/103 Verifying : perl-ExtUtils-Command-2:7.64-490.fc37.noarch 40/103 Verifying : perl-ExtUtils-Constant-0.25-492.fc38.noarch 41/103 Verifying : perl-ExtUtils-Embed-1.35-492.fc38.noarch 42/103 Verifying : perl-ExtUtils-Install-2.20-489.fc37.noarch 43/103 Verifying : perl-ExtUtils-MakeMaker-2:7.64-490.fc37.noarch 44/103 Verifying : perl-ExtUtils-Manifest-1:1.73-489.fc37.noarch 45/103 Verifying : perl-ExtUtils-ParseXS-1:3.45-489.fc37.noarch 46/103 Verifying : perl-Fcntl-1.15-492.fc38.x86_64 47/103 Verifying : perl-File-Basename-2.85-492.fc38.noarch 48/103 Verifying : perl-File-Compare-1.100.700-492.fc38.noarch 49/103 Verifying : perl-File-Copy-2.39-492.fc38.noarch 50/103 Verifying : perl-File-Find-1.40-492.fc38.noarch 51/103 Verifying : perl-File-Path-2.18-489.fc37.noarch 52/103 Verifying : perl-File-Temp-1:0.231.100-489.fc37.noarch 53/103 Verifying : perl-File-stat-1.12-492.fc38.noarch 54/103 Verifying : perl-FindBin-1.53-492.fc38.noarch 55/103 Verifying : perl-Getopt-Long-1:2.54-1.fc38.noarch 56/103 Verifying : perl-Getopt-Std-1.13-492.fc38.noarch 57/103 Verifying : perl-HTTP-Tiny-0.082-1.fc37.noarch 58/103 Verifying : perl-IO-1.50-492.fc38.x86_64 59/103 Verifying : perl-IPC-Open3-1.22-492.fc38.noarch 60/103 Verifying : perl-MIME-Base64-3.16-489.fc37.x86_64 61/103 Verifying : perl-POSIX-2.03-492.fc38.x86_64 62/103 Verifying : perl-PathTools-3.84-489.fc37.x86_64 63/103 Verifying : perl-Pod-Escapes-1:1.07-489.fc37.noarch 64/103 Verifying : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 65/103 Verifying : perl-Pod-Simple-1:3.43-490.fc37.noarch 66/103 Verifying : perl-Pod-Usage-4:2.03-3.fc37.noarch 67/103 Verifying : perl-Scalar-List-Utils-5:1.63-489.fc38.x86_64 68/103 Verifying : perl-SelectSaver-1.02-492.fc38.noarch 69/103 Verifying : perl-Socket-4:2.036-1.fc38.x86_64 70/103 Verifying : perl-Storable-1:3.26-489.fc37.x86_64 71/103 Verifying : perl-Symbol-1.09-492.fc38.noarch 72/103 Verifying : perl-Term-ANSIColor-5.01-490.fc37.noarch 73/103 Verifying : perl-Term-Cap-1.17-489.fc37.noarch 74/103 Verifying : perl-Test-Harness-1:3.44-490.fc37.noarch 75/103 Verifying : perl-Text-ParseWords-3.31-489.fc37.noarch 76/103 Verifying : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 77/103 Verifying : perl-Thread-Queue-3.14-489.fc37.noarch 78/103 Verifying : perl-Time-Local-2:1.300-489.fc37.noarch 79/103 Verifying : perl-base-2.27-492.fc38.noarch 80/103 Verifying : perl-constant-1.33-490.fc37.noarch 81/103 Verifying : perl-devel-4:5.36.0-492.fc38.x86_64 82/103 Verifying : perl-if-0.61.000-492.fc38.noarch 83/103 Verifying : perl-interpreter-4:5.36.0-492.fc38.x86_64 84/103 Verifying : perl-lib-0.65-492.fc38.x86_64 85/103 Verifying : perl-libs-4:5.36.0-492.fc38.x86_64 86/103 Verifying : perl-locale-1.10-492.fc38.noarch 87/103 Verifying : perl-mro-1.26-492.fc38.x86_64 88/103 Verifying : perl-overload-1.35-492.fc38.noarch 89/103 Verifying : perl-overloading-0.02-492.fc38.noarch 90/103 Verifying : perl-parent-1:0.239-1.fc38.noarch 91/103 Verifying : perl-podlators-1:5.00-1.fc38.noarch 92/103 Verifying : perl-threads-1:2.27-489.fc37.x86_64 93/103 Verifying : perl-threads-shared-1.64-489.fc37.x86_64 94/103 Verifying : perl-vars-1.05-492.fc38.noarch 95/103 Verifying : perl-version-8:0.99.29-490.fc37.x86_64 96/103 Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 97/103 Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 98/103 Verifying : python3-3.11.1-1.fc38.x86_64 99/103 Verifying : python3-libs-3.11.1-1.fc38.x86_64 100/103 Verifying : python3-pyparsing-3.0.9-2.fc37.noarch 101/103 Verifying : systemtap-sdt-devel-4.8~pre16650659g6a096a7d-1.f 102/103 Verifying : zlib-devel-1.2.13-1.fc38.x86_64 103/103 Installed: annobin-docs-10.99-1.0.1.fc38.noarch annobin-plugin-gcc-10.99-1.0.1.fc38.x86_64 autoconf-2.71-4.fc38.noarch automake-1.16.5-9.fc37.noarch cpp-13.0.0-0.4.fc38.x86_64 emacs-filesystem-1:28.1-3.fc37.noarch expat-2.5.0-1.fc38.x86_64 gc-8.2.2-1.fc38.x86_64 gcc-13.0.0-0.4.fc38.x86_64 gcc-plugin-annobin-13.0.0-0.4.fc38.x86_64 glibc-devel-2.36.9000-18.fc38.x86_64 glibc-headers-x86-2.36.9000-18.fc38.noarch groff-base-1.22.4-10.fc37.x86_64 gsl-2.7.1-2.fc38.x86_64 gsl-devel-2.7.1-2.fc38.x86_64 guile22-2.2.7-6.fc37.x86_64 htslib-1.15.1-1.fc38.x86_64 htslib-devel-1.15.1-1.fc38.x86_64 htslib-tools-1.15.1-1.fc38.x86_64 kernel-headers-6.1.0-1.fc38.x86_64 libb2-0.98.1-7.fc37.x86_64 libmpc-1.2.1-5.fc37.x86_64 libtool-ltdl-2.4.7-3.0.1.fc38.x86_64 libxcrypt-devel-4.4.33-5.fc38.x86_64 m4-1.4.19-4.fc37.x86_64 make-1:4.3-11.fc37.x86_64 mpdecimal-2.5.1-4.fc37.x86_64 ncurses-6.3-5.20221126.fc38.x86_64 perl-AutoSplit-5.74-492.fc38.noarch perl-B-1.83-492.fc38.x86_64 perl-Benchmark-1.23-492.fc38.noarch perl-Carp-1.52-489.fc37.noarch perl-Class-Struct-0.66-492.fc38.noarch perl-Data-Dumper-2.184-490.fc37.x86_64 perl-Devel-PPPort-3.68-490.fc37.x86_64 perl-DynaLoader-1.52-492.fc38.x86_64 perl-Encode-4:3.19-492.fc38.x86_64 perl-Errno-1.36-492.fc38.x86_64 perl-Exporter-5.77-489.fc37.noarch perl-ExtUtils-Command-2:7.64-490.fc37.noarch perl-ExtUtils-Constant-0.25-492.fc38.noarch perl-ExtUtils-Embed-1.35-492.fc38.noarch perl-ExtUtils-Install-2.20-489.fc37.noarch perl-ExtUtils-MakeMaker-2:7.64-490.fc37.noarch perl-ExtUtils-Manifest-1:1.73-489.fc37.noarch perl-ExtUtils-ParseXS-1:3.45-489.fc37.noarch perl-Fcntl-1.15-492.fc38.x86_64 perl-File-Basename-2.85-492.fc38.noarch perl-File-Compare-1.100.700-492.fc38.noarch perl-File-Copy-2.39-492.fc38.noarch perl-File-Find-1.40-492.fc38.noarch perl-File-Path-2.18-489.fc37.noarch perl-File-Temp-1:0.231.100-489.fc37.noarch perl-File-stat-1.12-492.fc38.noarch perl-FindBin-1.53-492.fc38.noarch perl-Getopt-Long-1:2.54-1.fc38.noarch perl-Getopt-Std-1.13-492.fc38.noarch perl-HTTP-Tiny-0.082-1.fc37.noarch perl-IO-1.50-492.fc38.x86_64 perl-IPC-Open3-1.22-492.fc38.noarch perl-MIME-Base64-3.16-489.fc37.x86_64 perl-POSIX-2.03-492.fc38.x86_64 perl-PathTools-3.84-489.fc37.x86_64 perl-Pod-Escapes-1:1.07-489.fc37.noarch perl-Pod-Perldoc-3.28.01-490.fc37.noarch perl-Pod-Simple-1:3.43-490.fc37.noarch perl-Pod-Usage-4:2.03-3.fc37.noarch perl-Scalar-List-Utils-5:1.63-489.fc38.x86_64 perl-SelectSaver-1.02-492.fc38.noarch perl-Socket-4:2.036-1.fc38.x86_64 perl-Storable-1:3.26-489.fc37.x86_64 perl-Symbol-1.09-492.fc38.noarch perl-Term-ANSIColor-5.01-490.fc37.noarch perl-Term-Cap-1.17-489.fc37.noarch perl-Test-Harness-1:3.44-490.fc37.noarch perl-Text-ParseWords-3.31-489.fc37.noarch perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch perl-Thread-Queue-3.14-489.fc37.noarch perl-Time-Local-2:1.300-489.fc37.noarch perl-base-2.27-492.fc38.noarch perl-constant-1.33-490.fc37.noarch perl-devel-4:5.36.0-492.fc38.x86_64 perl-if-0.61.000-492.fc38.noarch perl-interpreter-4:5.36.0-492.fc38.x86_64 perl-lib-0.65-492.fc38.x86_64 perl-libs-4:5.36.0-492.fc38.x86_64 perl-locale-1.10-492.fc38.noarch perl-mro-1.26-492.fc38.x86_64 perl-overload-1.35-492.fc38.noarch perl-overloading-0.02-492.fc38.noarch perl-parent-1:0.239-1.fc38.noarch perl-podlators-1:5.00-1.fc38.noarch perl-threads-1:2.27-489.fc37.x86_64 perl-threads-shared-1.64-489.fc37.x86_64 perl-vars-1.05-492.fc38.noarch perl-version-8:0.99.29-490.fc37.x86_64 python-pip-wheel-22.3.1-1.fc38.noarch python-setuptools-wheel-65.5.1-1.fc38.noarch python3-3.11.1-1.fc38.x86_64 python3-libs-3.11.1-1.fc38.x86_64 python3-pyparsing-3.0.9-2.fc37.noarch systemtap-sdt-devel-4.8~pre16650659g6a096a7d-1.fc38.x86_64 zlib-devel-1.2.13-1.fc38.x86_64 Complete! Finish: build setup for bcftools-1.15.1-2.fc38.src.rpm Start: rpmbuild bcftools-1.15.1-2.fc38.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1661212800 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.t1AR9m + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/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):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 Patch #0 (bcftools-1.15.1-aarch64-fix-vcf_plugin-tests.patch): 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.pMYm9d + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 2022-12-23 11:40:44.512310550 +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=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 x86_64-redhat-linux-gnu-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether 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 -j2 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o tabix.o tabix.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfindex.o vcfindex.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfisec.o vcfisec.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfstats.o vcfstats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfquery.o vcfquery.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcffilter.o vcffilter.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfmerge.o vcfmerge.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfsom.o vcfsom.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -c -o filter.o filter.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfgtcheck.o vcfgtcheck.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfnorm.o vcfnorm.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfview.o vcfview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfroh.o vcfroh.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfconcat.o vcfconcat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfannotate.o vcfannotate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfcall.o vcfcall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcmp.o vcmp.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o gvcf.o gvcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o mcall.o mcall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o reheader.o reheader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfconvert.o vcfconvert.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o tsv2vcf.o tsv2vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o convert.o convert.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfhead.o vcfhead.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfcnv.o vcfcnv.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o HMM.o HMM.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o ploidy.o ploidy.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o bin.o bin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o consensus.o consensus.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o version.o version.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o hclust.o hclust.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o smpl_ilist.o smpl_ilist.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfbuf.o vcfbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o mpileup.o mpileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o bam2bcf.o bam2bcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o csq.o csq.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfsort.o vcfsort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o cols.o cols.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o extsort.o extsort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o bam_sample.o bam_sample.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o dist.o dist.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o ccall.o ccall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o em.o em.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o abuf.o abuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o kmin.o kmin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o prob1.o prob1.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o str_finder.o str_finder.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o peakfit.o peakfit.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o polysomy.o polysomy.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o test/test-rbuf.o test/test-rbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -DPLUGINPATH='"/usr/local/libexec/bcftools:/usr/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -DUSE_GPL -c -o main.o main.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -rdynamic -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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,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,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.XMhMHX + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64 ++ dirname /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/bin /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/share/man/man1 /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools /usr/bin/install -p bcftools /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/bin /usr/bin/install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/bin /usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/share/man/man1 /usr/bin/install -p plugins/*.so /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.15.1-2.fc38 --unique-debug-suffix -1.15.1-2.fc38.x86_64 --unique-debug-src-base bcftools-1.15.1-2.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/bcftools-1.15.1 extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/bin/bcftools extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/GTisec.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/GTsubset.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/ad-bias.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/add-variantkey.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/af-dist.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/allele-length.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/check-ploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/check-sparsity.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/color-chrs.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/contrast.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/counts.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/dosage.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/fill-AN-AC.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/fill-from-fasta.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/fill-tags.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/fixploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/fixref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/frameshifts.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/guess-ploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/gvcfz.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/impute-info.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/indel-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/isecGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/mendelian.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/missing2ref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/parental-origin.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/prune.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/remove-overlaps.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/scatter.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/setGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/smpl-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/split-vep.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/split.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/tag2tag.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/trio-dnm2.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/trio-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/trio-switch-rate.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/libexec/bcftools/variantkey-hex.so original debug info size: 6200kB, size after compression: 5404kB /usr/bin/sepdebugcrcfix: Updated 39 CRC32s, 0 CRC32s did match. 5400 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.09twDG + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 + grep -E '/lib(64)?/libhts\.so\.' + ldd bcftools libhts.so.3 => /lib64/libhts.so.3 (0x00007fe42e6fd000) + 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/3SiBnGXvSN/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/3SiBnGXvSN/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/3SiBnGXvSN/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/3SiBnGXvSN/merge.a.bcf 1:3000151-3000151 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/3SiBnGXvSN/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/3SiBnGXvSN/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/3SiBnGXvSN/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/3SiBnGXvSN/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/3SiBnGXvSN/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/3SiBnGXvSN/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/3SiBnGXvSN/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/3SiBnGXvSN/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/3SiBnGXvSN/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/3SiBnGXvSN/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -s /tmp/3SiBnGXvSN/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -s /tmp/3SiBnGXvSN/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -s /tmp/3SiBnGXvSN/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/3SiBnGXvSN/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/3SiBnGXvSN/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/3SiBnGXvSN/idx.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/3SiBnGXvSN/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/3SiBnGXvSN/idx.bcf.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -s /tmp/3SiBnGXvSN/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -s /tmp/3SiBnGXvSN/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -s /tmp/3SiBnGXvSN/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/3SiBnGXvSN/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/3SiBnGXvSN/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/3SiBnGXvSN/empty.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/3SiBnGXvSN/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/3SiBnGXvSN/empty.bcf.csi .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.15.1/bcftools stats -s - /tmp/3SiBnGXvSN/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/check.vcf.gz | /builddir/build/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/misc/plot-vcfstats -m /tmp/3SiBnGXvSN/check.1.chk /tmp/3SiBnGXvSN/check.2.chk /tmp/3SiBnGXvSN/check.3.chk /tmp/3SiBnGXvSN/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/bcftools stats -s - /tmp/3SiBnGXvSN/stats.a.vcf.gz /tmp/3SiBnGXvSN/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.15.1/bcftools stats -s B /tmp/3SiBnGXvSN/stats.a.vcf.gz /tmp/3SiBnGXvSN/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.15.1/bcftools stats -s - /tmp/3SiBnGXvSN/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -n =2 /tmp/3SiBnGXvSN/isec.a.vcf.gz /tmp/3SiBnGXvSN/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -n =2 /tmp/3SiBnGXvSN/isec.a.vcf.gz /tmp/3SiBnGXvSN/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/3SiBnGXvSN/isec.a.vcf.gz /tmp/3SiBnGXvSN/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/3SiBnGXvSN/isec.a.vcf.gz /tmp/3SiBnGXvSN/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -n =2 -c both /tmp/3SiBnGXvSN/isec.a.vcf.gz /tmp/3SiBnGXvSN/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -n =2 -c both /tmp/3SiBnGXvSN/isec.a.vcf.gz /tmp/3SiBnGXvSN/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -n =2 -c any /tmp/3SiBnGXvSN/isec.a.vcf.gz /tmp/3SiBnGXvSN/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -n =2 -c any /tmp/3SiBnGXvSN/isec.a.vcf.gz /tmp/3SiBnGXvSN/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -C -c any /tmp/3SiBnGXvSN/isec.a.vcf.gz /tmp/3SiBnGXvSN/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -C -c any /tmp/3SiBnGXvSN/isec.a.vcf.gz /tmp/3SiBnGXvSN/isec.b.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec --no-version -T /tmp/3SiBnGXvSN/isec.tab.gz /tmp/3SiBnGXvSN/isec.a.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -T /tmp/3SiBnGXvSN/isec.tab.gz /tmp/3SiBnGXvSN/isec.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/3SiBnGXvSN/isec-miss.1.1.vcf.gz /tmp/3SiBnGXvSN/isec-miss.1.2.vcf.gz /tmp/3SiBnGXvSN/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/3SiBnGXvSN/isec-miss.1.1.vcf.gz /tmp/3SiBnGXvSN/isec-miss.1.2.vcf.gz /tmp/3SiBnGXvSN/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -R /builddir/build/BUILD/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/3SiBnGXvSN/isec-miss.1.1.vcf.gz /tmp/3SiBnGXvSN/isec-miss.1.2.vcf.gz /tmp/3SiBnGXvSN/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/3SiBnGXvSN/isec-miss.1.1.vcf.gz /tmp/3SiBnGXvSN/isec-miss.1.2.vcf.gz /tmp/3SiBnGXvSN/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/3SiBnGXvSN/isec-miss.2.1.vcf.gz /tmp/3SiBnGXvSN/isec-miss.2.2.vcf.gz /tmp/3SiBnGXvSN/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/3SiBnGXvSN/isec-miss.2.1.vcf.gz /tmp/3SiBnGXvSN/isec-miss.2.2.vcf.gz /tmp/3SiBnGXvSN/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -R /builddir/build/BUILD/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/3SiBnGXvSN/isec-miss.2.1.vcf.gz /tmp/3SiBnGXvSN/isec-miss.2.2.vcf.gz /tmp/3SiBnGXvSN/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/3SiBnGXvSN/isec-miss.2.1.vcf.gz /tmp/3SiBnGXvSN/isec-miss.2.2.vcf.gz /tmp/3SiBnGXvSN/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -i AF:join /tmp/3SiBnGXvSN/merge.join.a.vcf.gz /tmp/3SiBnGXvSN/merge.join.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -i AF:join /tmp/3SiBnGXvSN/merge.join.a.vcf.gz /tmp/3SiBnGXvSN/merge.join.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -i AF:join /tmp/3SiBnGXvSN/merge.join.a.bcf /tmp/3SiBnGXvSN/merge.join.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -i AF:join /tmp/3SiBnGXvSN/merge.join.a.bcf /tmp/3SiBnGXvSN/merge.join.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/3SiBnGXvSN/merge.LPL.a.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.b.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/3SiBnGXvSN/merge.LPL.a.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.b.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/3SiBnGXvSN/merge.LPL.a.bcf /tmp/3SiBnGXvSN/merge.LPL.b.bcf /tmp/3SiBnGXvSN/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/3SiBnGXvSN/merge.LPL.a.bcf /tmp/3SiBnGXvSN/merge.LPL.b.bcf /tmp/3SiBnGXvSN/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 1 /tmp/3SiBnGXvSN/merge.LPL.a.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.b.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 1 /tmp/3SiBnGXvSN/merge.LPL.a.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.b.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 1 /tmp/3SiBnGXvSN/merge.LPL.a.bcf /tmp/3SiBnGXvSN/merge.LPL.b.bcf /tmp/3SiBnGXvSN/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 1 /tmp/3SiBnGXvSN/merge.LPL.a.bcf /tmp/3SiBnGXvSN/merge.LPL.b.bcf /tmp/3SiBnGXvSN/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 2 /tmp/3SiBnGXvSN/merge.LPL.a.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.b.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 2 /tmp/3SiBnGXvSN/merge.LPL.a.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.b.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 2 /tmp/3SiBnGXvSN/merge.LPL.a.bcf /tmp/3SiBnGXvSN/merge.LPL.b.bcf /tmp/3SiBnGXvSN/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 2 /tmp/3SiBnGXvSN/merge.LPL.a.bcf /tmp/3SiBnGXvSN/merge.LPL.b.bcf /tmp/3SiBnGXvSN/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 3 /tmp/3SiBnGXvSN/merge.LPL.a.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.b.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 3 /tmp/3SiBnGXvSN/merge.LPL.a.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.b.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 3 /tmp/3SiBnGXvSN/merge.LPL.a.bcf /tmp/3SiBnGXvSN/merge.LPL.b.bcf /tmp/3SiBnGXvSN/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 3 /tmp/3SiBnGXvSN/merge.LPL.a.bcf /tmp/3SiBnGXvSN/merge.LPL.b.bcf /tmp/3SiBnGXvSN/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 4 /tmp/3SiBnGXvSN/merge.LPL.a.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.b.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 4 /tmp/3SiBnGXvSN/merge.LPL.a.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.b.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 4 /tmp/3SiBnGXvSN/merge.LPL.a.bcf /tmp/3SiBnGXvSN/merge.LPL.b.bcf /tmp/3SiBnGXvSN/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 4 /tmp/3SiBnGXvSN/merge.LPL.a.bcf /tmp/3SiBnGXvSN/merge.LPL.b.bcf /tmp/3SiBnGXvSN/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 5 /tmp/3SiBnGXvSN/merge.LPL.a.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.b.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 5 /tmp/3SiBnGXvSN/merge.LPL.a.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.b.vcf.gz /tmp/3SiBnGXvSN/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 5 /tmp/3SiBnGXvSN/merge.LPL.a.bcf /tmp/3SiBnGXvSN/merge.LPL.b.bcf /tmp/3SiBnGXvSN/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 5 /tmp/3SiBnGXvSN/merge.LPL.a.bcf /tmp/3SiBnGXvSN/merge.LPL.b.bcf /tmp/3SiBnGXvSN/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/3SiBnGXvSN/merge.a.vcf.gz /tmp/3SiBnGXvSN/merge.b.vcf.gz /tmp/3SiBnGXvSN/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/3SiBnGXvSN/merge.a.vcf.gz /tmp/3SiBnGXvSN/merge.b.vcf.gz /tmp/3SiBnGXvSN/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/3SiBnGXvSN/merge.a.bcf /tmp/3SiBnGXvSN/merge.b.bcf /tmp/3SiBnGXvSN/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/3SiBnGXvSN/merge.a.bcf /tmp/3SiBnGXvSN/merge.b.bcf /tmp/3SiBnGXvSN/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -Fx /tmp/3SiBnGXvSN/merge.a.vcf.gz /tmp/3SiBnGXvSN/merge.b.vcf.gz /tmp/3SiBnGXvSN/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -Fx /tmp/3SiBnGXvSN/merge.a.vcf.gz /tmp/3SiBnGXvSN/merge.b.vcf.gz /tmp/3SiBnGXvSN/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -Fx /tmp/3SiBnGXvSN/merge.a.bcf /tmp/3SiBnGXvSN/merge.b.bcf /tmp/3SiBnGXvSN/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -Fx /tmp/3SiBnGXvSN/merge.a.bcf /tmp/3SiBnGXvSN/merge.b.bcf /tmp/3SiBnGXvSN/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -0 /tmp/3SiBnGXvSN/merge.a.vcf.gz /tmp/3SiBnGXvSN/merge.b.vcf.gz /tmp/3SiBnGXvSN/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -0 /tmp/3SiBnGXvSN/merge.a.vcf.gz /tmp/3SiBnGXvSN/merge.b.vcf.gz /tmp/3SiBnGXvSN/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -0 /tmp/3SiBnGXvSN/merge.a.bcf /tmp/3SiBnGXvSN/merge.b.bcf /tmp/3SiBnGXvSN/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -0 /tmp/3SiBnGXvSN/merge.a.bcf /tmp/3SiBnGXvSN/merge.b.bcf /tmp/3SiBnGXvSN/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m none /tmp/3SiBnGXvSN/merge.2.a.vcf.gz /tmp/3SiBnGXvSN/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m none /tmp/3SiBnGXvSN/merge.2.a.vcf.gz /tmp/3SiBnGXvSN/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m none /tmp/3SiBnGXvSN/merge.2.a.bcf /tmp/3SiBnGXvSN/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m none /tmp/3SiBnGXvSN/merge.2.a.bcf /tmp/3SiBnGXvSN/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m both /tmp/3SiBnGXvSN/merge.2.a.vcf.gz /tmp/3SiBnGXvSN/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m both /tmp/3SiBnGXvSN/merge.2.a.vcf.gz /tmp/3SiBnGXvSN/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m both /tmp/3SiBnGXvSN/merge.2.a.bcf /tmp/3SiBnGXvSN/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m both /tmp/3SiBnGXvSN/merge.2.a.bcf /tmp/3SiBnGXvSN/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m all /tmp/3SiBnGXvSN/merge.2.a.vcf.gz /tmp/3SiBnGXvSN/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m all /tmp/3SiBnGXvSN/merge.2.a.vcf.gz /tmp/3SiBnGXvSN/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m all /tmp/3SiBnGXvSN/merge.2.a.bcf /tmp/3SiBnGXvSN/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m all /tmp/3SiBnGXvSN/merge.2.a.bcf /tmp/3SiBnGXvSN/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/3SiBnGXvSN/merge.3.a.vcf.gz /tmp/3SiBnGXvSN/merge.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/3SiBnGXvSN/merge.3.a.vcf.gz /tmp/3SiBnGXvSN/merge.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/3SiBnGXvSN/merge.3.a.bcf /tmp/3SiBnGXvSN/merge.3.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/3SiBnGXvSN/merge.3.a.bcf /tmp/3SiBnGXvSN/merge.3.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m id /tmp/3SiBnGXvSN/merge.4.a.vcf.gz /tmp/3SiBnGXvSN/merge.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m id /tmp/3SiBnGXvSN/merge.4.a.vcf.gz /tmp/3SiBnGXvSN/merge.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m id /tmp/3SiBnGXvSN/merge.4.a.bcf /tmp/3SiBnGXvSN/merge.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m id /tmp/3SiBnGXvSN/merge.4.a.bcf /tmp/3SiBnGXvSN/merge.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/3SiBnGXvSN/gvcf.merge.1.vcf.gz /tmp/3SiBnGXvSN/gvcf.merge.2.vcf.gz /tmp/3SiBnGXvSN/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/3SiBnGXvSN/gvcf.merge.1.vcf.gz /tmp/3SiBnGXvSN/gvcf.merge.2.vcf.gz /tmp/3SiBnGXvSN/gvcf.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/3SiBnGXvSN/gvcf.merge.1.bcf /tmp/3SiBnGXvSN/gvcf.merge.2.bcf /tmp/3SiBnGXvSN/gvcf.merge.3.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/3SiBnGXvSN/gvcf.merge.1.bcf /tmp/3SiBnGXvSN/gvcf.merge.2.bcf /tmp/3SiBnGXvSN/gvcf.merge.3.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.2.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.2.b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.2.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.2.b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - -i SRC:join /tmp/3SiBnGXvSN/merge.gvcf.3.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - -i SRC:join /tmp/3SiBnGXvSN/merge.gvcf.3.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.4.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.4.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.4.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.4.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/3SiBnGXvSN/merge.5.a.vcf.gz /tmp/3SiBnGXvSN/merge.5.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/3SiBnGXvSN/merge.5.a.vcf.gz /tmp/3SiBnGXvSN/merge.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/3SiBnGXvSN/merge.5.a.bcf /tmp/3SiBnGXvSN/merge.5.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/3SiBnGXvSN/merge.5.a.bcf /tmp/3SiBnGXvSN/merge.5.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/3SiBnGXvSN/merge.6.a.vcf.gz /tmp/3SiBnGXvSN/merge.6.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/3SiBnGXvSN/merge.6.a.vcf.gz /tmp/3SiBnGXvSN/merge.6.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/3SiBnGXvSN/merge.6.a.bcf /tmp/3SiBnGXvSN/merge.6.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/3SiBnGXvSN/merge.6.a.bcf /tmp/3SiBnGXvSN/merge.6.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.7.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.7.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.7.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.7.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.7.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.8.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.8.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.8.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/3SiBnGXvSN/merge.gvcf.8.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/3SiBnGXvSN/merge.7.a.vcf.gz /tmp/3SiBnGXvSN/merge.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/3SiBnGXvSN/merge.7.a.vcf.gz /tmp/3SiBnGXvSN/merge.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/3SiBnGXvSN/merge.7.a.bcf /tmp/3SiBnGXvSN/merge.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/3SiBnGXvSN/merge.7.a.bcf /tmp/3SiBnGXvSN/merge.7.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/3SiBnGXvSN/merge.gvcf.9a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9c.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/3SiBnGXvSN/merge.gvcf.9a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9c.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/3SiBnGXvSN/merge.gvcf.9a.bcf /tmp/3SiBnGXvSN/merge.gvcf.9b.bcf /tmp/3SiBnGXvSN/merge.gvcf.9c.bcf /tmp/3SiBnGXvSN/merge.gvcf.9d.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/3SiBnGXvSN/merge.gvcf.9a.bcf /tmp/3SiBnGXvSN/merge.gvcf.9b.bcf /tmp/3SiBnGXvSN/merge.gvcf.9c.bcf /tmp/3SiBnGXvSN/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/3SiBnGXvSN/merge.gvcf.9a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9c.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/3SiBnGXvSN/merge.gvcf.9a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9c.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/3SiBnGXvSN/merge.gvcf.9a.bcf /tmp/3SiBnGXvSN/merge.gvcf.9b.bcf /tmp/3SiBnGXvSN/merge.gvcf.9c.bcf /tmp/3SiBnGXvSN/merge.gvcf.9d.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/3SiBnGXvSN/merge.gvcf.9a.bcf /tmp/3SiBnGXvSN/merge.gvcf.9b.bcf /tmp/3SiBnGXvSN/merge.gvcf.9c.bcf /tmp/3SiBnGXvSN/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/3SiBnGXvSN/merge.gvcf.9a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9c.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9d.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/3SiBnGXvSN/merge.gvcf.9a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9c.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9d.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/3SiBnGXvSN/merge.gvcf.9a.bcf /tmp/3SiBnGXvSN/merge.gvcf.9b.bcf /tmp/3SiBnGXvSN/merge.gvcf.9c.bcf /tmp/3SiBnGXvSN/merge.gvcf.9d.bcf /tmp/3SiBnGXvSN/merge.gvcf.9e.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/3SiBnGXvSN/merge.gvcf.9a.bcf /tmp/3SiBnGXvSN/merge.gvcf.9b.bcf /tmp/3SiBnGXvSN/merge.gvcf.9c.bcf /tmp/3SiBnGXvSN/merge.gvcf.9d.bcf /tmp/3SiBnGXvSN/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/3SiBnGXvSN/merge.gvcf.9a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9c.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9d.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/3SiBnGXvSN/merge.gvcf.9a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9c.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9d.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/3SiBnGXvSN/merge.gvcf.9a.bcf /tmp/3SiBnGXvSN/merge.gvcf.9b.bcf /tmp/3SiBnGXvSN/merge.gvcf.9c.bcf /tmp/3SiBnGXvSN/merge.gvcf.9d.bcf /tmp/3SiBnGXvSN/merge.gvcf.9e.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/3SiBnGXvSN/merge.gvcf.9a.bcf /tmp/3SiBnGXvSN/merge.gvcf.9b.bcf /tmp/3SiBnGXvSN/merge.gvcf.9c.bcf /tmp/3SiBnGXvSN/merge.gvcf.9d.bcf /tmp/3SiBnGXvSN/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/3SiBnGXvSN/merge.gvcf.10.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/3SiBnGXvSN/merge.gvcf.10.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/3SiBnGXvSN/merge.gvcf.10.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/3SiBnGXvSN/merge.gvcf.10.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -m none /tmp/3SiBnGXvSN/merge.gvcf.10.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -m none /tmp/3SiBnGXvSN/merge.gvcf.10.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -m none /tmp/3SiBnGXvSN/merge.gvcf.10.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -m none /tmp/3SiBnGXvSN/merge.gvcf.10.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/3SiBnGXvSN/merge.gvcf.10.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/3SiBnGXvSN/merge.gvcf.10.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/3SiBnGXvSN/merge.gvcf.10.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/3SiBnGXvSN/merge.gvcf.10.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/3SiBnGXvSN/merge.gvcf.10.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/3SiBnGXvSN/merge.gvcf.10.a.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/3SiBnGXvSN/merge.gvcf.10.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/3SiBnGXvSN/merge.gvcf.10.a.bcf /tmp/3SiBnGXvSN/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/3SiBnGXvSN/merge.gvcf.10.b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/3SiBnGXvSN/merge.gvcf.10.b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/3SiBnGXvSN/merge.gvcf.10.b.bcf /tmp/3SiBnGXvSN/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/3SiBnGXvSN/merge.gvcf.10.b.bcf /tmp/3SiBnGXvSN/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/3SiBnGXvSN/merge.gvcf.10.b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/3SiBnGXvSN/merge.gvcf.10.b.vcf.gz /tmp/3SiBnGXvSN/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/3SiBnGXvSN/merge.gvcf.10.b.bcf /tmp/3SiBnGXvSN/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/3SiBnGXvSN/merge.gvcf.10.b.bcf /tmp/3SiBnGXvSN/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/3SiBnGXvSN/merge.noidx.a.vcf.gz /tmp/3SiBnGXvSN/merge.noidx.b.vcf.gz /tmp/3SiBnGXvSN/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/3SiBnGXvSN/merge.noidx.a.vcf.gz /tmp/3SiBnGXvSN/merge.noidx.b.vcf.gz /tmp/3SiBnGXvSN/merge.noidx.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/3SiBnGXvSN/merge.noidx.a.bcf /tmp/3SiBnGXvSN/merge.noidx.b.bcf /tmp/3SiBnGXvSN/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/3SiBnGXvSN/merge.noidx.a.bcf /tmp/3SiBnGXvSN/merge.noidx.b.bcf /tmp/3SiBnGXvSN/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --no-index /builddir/build/BUILD/bcftools-1.15.1/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.15.1/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.15.1/test/merge.noidx.c.vcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --no-index /builddir/build/BUILD/bcftools-1.15.1/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.15.1/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.15.1/test/merge.noidx.c.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --no-index /tmp/3SiBnGXvSN/merge.noidx.a.bcf /tmp/3SiBnGXvSN/merge.noidx.b.bcf /tmp/3SiBnGXvSN/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --no-index /tmp/3SiBnGXvSN/merge.noidx.a.bcf /tmp/3SiBnGXvSN/merge.noidx.b.bcf /tmp/3SiBnGXvSN/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/3SiBnGXvSN/merge.8.a.vcf.gz /tmp/3SiBnGXvSN/merge.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/3SiBnGXvSN/merge.8.a.vcf.gz /tmp/3SiBnGXvSN/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/3SiBnGXvSN/merge.8.a.bcf /tmp/3SiBnGXvSN/merge.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/3SiBnGXvSN/merge.8.a.bcf /tmp/3SiBnGXvSN/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/3SiBnGXvSN/merge.8.a.vcf.gz /tmp/3SiBnGXvSN/merge.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/3SiBnGXvSN/merge.8.a.vcf.gz /tmp/3SiBnGXvSN/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/3SiBnGXvSN/merge.8.a.bcf /tmp/3SiBnGXvSN/merge.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/3SiBnGXvSN/merge.8.a.bcf /tmp/3SiBnGXvSN/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/3SiBnGXvSN/merge.9.a.vcf.gz /tmp/3SiBnGXvSN/merge.9.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/3SiBnGXvSN/merge.9.a.vcf.gz /tmp/3SiBnGXvSN/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/3SiBnGXvSN/merge.9.a.bcf /tmp/3SiBnGXvSN/merge.9.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/3SiBnGXvSN/merge.9.a.bcf /tmp/3SiBnGXvSN/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/3SiBnGXvSN/merge.9.a.vcf.gz /tmp/3SiBnGXvSN/merge.9.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/3SiBnGXvSN/merge.9.a.vcf.gz /tmp/3SiBnGXvSN/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/3SiBnGXvSN/merge.9.a.bcf /tmp/3SiBnGXvSN/merge.9.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/3SiBnGXvSN/merge.9.a.bcf /tmp/3SiBnGXvSN/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/3SiBnGXvSN/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.string.vcf.gz | /builddir/build/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/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/3SiBnGXvSN/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.string.vcf.gz | /builddir/build/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/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/3SiBnGXvSN/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.string.vcf.gz | /builddir/build/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/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/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/bcftools query -f '%RSX\t%VKX\n' /tmp/3SiBnGXvSN/query.variantkey.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.variantkey.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/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/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/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/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/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/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/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/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/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/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/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/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/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/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/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/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/3SiBnGXvSN/view.vectors.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.vectors.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/3SiBnGXvSN/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/3SiBnGXvSN/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/3SiBnGXvSN/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/3SiBnGXvSN/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.vcf.gz | /builddir/build/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/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/3SiBnGXvSN/query.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.2.vcf.gz | /builddir/build/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/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/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/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/3SiBnGXvSN/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/filter.11.vcf.gz | /builddir/build/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/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/3SiBnGXvSN/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/filter.11.vcf.gz | /builddir/build/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/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/3SiBnGXvSN/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/filter.11.vcf.gz | /builddir/build/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/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/3SiBnGXvSN/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/filter.11.vcf.gz | /builddir/build/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/bcftools query -f'%LINE' /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%LINE' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/3SiBnGXvSN/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter-type.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/3SiBnGXvSN/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter-type.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/3SiBnGXvSN/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter-type.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/3SiBnGXvSN/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter-type.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/3SiBnGXvSN/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter-type.vcf.gz | /builddir/build/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/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/3SiBnGXvSN/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/filter-missing-floats.vcf.gz | /builddir/build/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/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/3SiBnGXvSN/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/filter-missing-floats.vcf.gz | /builddir/build/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/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/3SiBnGXvSN/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/missing.vcf.gz | /builddir/build/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/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/3SiBnGXvSN/query.filter.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.2.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/3SiBnGXvSN/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/filter.5.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/3SiBnGXvSN/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/filter.5.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.filter.vcf.gz | /builddir/build/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/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/3SiBnGXvSN/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.3.vcf.gz | /builddir/build/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/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/3SiBnGXvSN/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.3.vcf.gz | /builddir/build/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/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/3SiBnGXvSN/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.3.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/3SiBnGXvSN/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/filter.5.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/3SiBnGXvSN/query.filter.4.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.4.vcf.gz | /builddir/build/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/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.15.1/test/query.56.out' /tmp/3SiBnGXvSN/view.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.15.1/test/query.56.out' .. ok test_vcf_query: /builddir/build/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/3SiBnGXvSN/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.5.vcf.gz | /builddir/build/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/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/3SiBnGXvSN/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.5.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/3SiBnGXvSN/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.5.vcf.gz | /builddir/build/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/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/3SiBnGXvSN/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.negative.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/3SiBnGXvSN/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.negative.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/3SiBnGXvSN/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.negative.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/3SiBnGXvSN/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.negative.vcf.gz | /builddir/build/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/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/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/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/3SiBnGXvSN/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.11.vcf.gz | /builddir/build/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/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/3SiBnGXvSN/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.11.vcf.gz | /builddir/build/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/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/3SiBnGXvSN/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.11.vcf.gz | /builddir/build/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/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/3SiBnGXvSN/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.11.vcf.gz | /builddir/build/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/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' /tmp/3SiBnGXvSN/query.pbinom.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.pbinom.1.vcf.gz | /builddir/build/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/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/3SiBnGXvSN/query.filter.6.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.6.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/3SiBnGXvSN/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.7.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/3SiBnGXvSN/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.7.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/3SiBnGXvSN/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.7.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/3SiBnGXvSN/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.7.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/3SiBnGXvSN/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.7.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/3SiBnGXvSN/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.7.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/3SiBnGXvSN/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.7.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/3SiBnGXvSN/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.7.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/3SiBnGXvSN/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.8.vcf.gz | /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/3SiBnGXvSN/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.8.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/3SiBnGXvSN/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.9.vcf.gz | /builddir/build/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/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/3SiBnGXvSN/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.9.vcf.gz | /builddir/build/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/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/3SiBnGXvSN/query.filter.13.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.13.vcf.gz | /builddir/build/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/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/3SiBnGXvSN/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.10.vcf.gz | /builddir/build/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/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/3SiBnGXvSN/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.10.vcf.gz | /builddir/build/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/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/3SiBnGXvSN/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.vcf.gz | /builddir/build/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/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/3SiBnGXvSN/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.12.vcf.gz | /builddir/build/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/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/3SiBnGXvSN/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.12.vcf.gz | /builddir/build/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/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt /tmp/3SiBnGXvSN/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt /tmp/3SiBnGXvSN/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt /tmp/3SiBnGXvSN/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt /tmp/3SiBnGXvSN/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.txt /tmp/3SiBnGXvSN/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.txt /tmp/3SiBnGXvSN/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/3SiBnGXvSN/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/3SiBnGXvSN/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -cx -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/3SiBnGXvSN/norm.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -cx -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/3SiBnGXvSN/norm.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/3SiBnGXvSN/norm.split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/3SiBnGXvSN/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/3SiBnGXvSN/norm.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/3SiBnGXvSN/norm.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m- --force /tmp/3SiBnGXvSN/norm.split.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m- --force /tmp/3SiBnGXvSN/norm.split.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/3SiBnGXvSN/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/3SiBnGXvSN/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m- --keep-sum AD /tmp/3SiBnGXvSN/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m- --keep-sum AD /tmp/3SiBnGXvSN/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/3SiBnGXvSN/norm.split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/3SiBnGXvSN/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/3SiBnGXvSN/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/3SiBnGXvSN/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/3SiBnGXvSN/norm.merge.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/3SiBnGXvSN/norm.merge.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/3SiBnGXvSN/norm.merge.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/3SiBnGXvSN/norm.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m+ -s /tmp/3SiBnGXvSN/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m+ -s /tmp/3SiBnGXvSN/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -Nc s -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/3SiBnGXvSN/norm.setref.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -Nc s -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/3SiBnGXvSN/norm.setref.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/3SiBnGXvSN/norm.telomere.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/3SiBnGXvSN/norm.telomere.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d snps /tmp/3SiBnGXvSN/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d snps /tmp/3SiBnGXvSN/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d indels /tmp/3SiBnGXvSN/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d indels /tmp/3SiBnGXvSN/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d both /tmp/3SiBnGXvSN/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d both /tmp/3SiBnGXvSN/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d all /tmp/3SiBnGXvSN/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d all /tmp/3SiBnGXvSN/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d none /tmp/3SiBnGXvSN/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d none /tmp/3SiBnGXvSN/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d exact /tmp/3SiBnGXvSN/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d exact /tmp/3SiBnGXvSN/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d none /tmp/3SiBnGXvSN/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d none /tmp/3SiBnGXvSN/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d exact /tmp/3SiBnGXvSN/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d exact /tmp/3SiBnGXvSN/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d indels /tmp/3SiBnGXvSN/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d indels /tmp/3SiBnGXvSN/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d any /tmp/3SiBnGXvSN/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d any /tmp/3SiBnGXvSN/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d both /tmp/3SiBnGXvSN/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d both /tmp/3SiBnGXvSN/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d snps /tmp/3SiBnGXvSN/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d snps /tmp/3SiBnGXvSN/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -c s -a -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.2.fa /tmp/3SiBnGXvSN/norm.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -c s -a -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.2.fa /tmp/3SiBnGXvSN/norm.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -c s -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.iupac.fa /tmp/3SiBnGXvSN/norm.iupac.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -c s -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.iupac.fa /tmp/3SiBnGXvSN/norm.iupac.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -c s -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.3.fa /tmp/3SiBnGXvSN/norm.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -c s -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.3.fa /tmp/3SiBnGXvSN/norm.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/3SiBnGXvSN/atomize.split.1.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/3SiBnGXvSN/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/3SiBnGXvSN/atomize.split.1.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/3SiBnGXvSN/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/3SiBnGXvSN/atomize.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/3SiBnGXvSN/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/3SiBnGXvSN/atomize.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/3SiBnGXvSN/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . /tmp/3SiBnGXvSN/atomize.split.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . /tmp/3SiBnGXvSN/atomize.split.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m +both /tmp/3SiBnGXvSN/norm.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m +both /tmp/3SiBnGXvSN/norm.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m +any /tmp/3SiBnGXvSN/norm.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m +any /tmp/3SiBnGXvSN/norm.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/3SiBnGXvSN/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/3SiBnGXvSN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -f PASS -Xks NA00003 /tmp/3SiBnGXvSN/view.vcf.gz -r20,Y .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -f PASS -Xks NA00003 /tmp/3SiBnGXvSN/view.vcf.gz -r20,Y | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -xs NA00003 /tmp/3SiBnGXvSN/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -xs NA00003 /tmp/3SiBnGXvSN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/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/3SiBnGXvSN/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/3SiBnGXvSN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -p /tmp/3SiBnGXvSN/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -p /tmp/3SiBnGXvSN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -P /tmp/3SiBnGXvSN/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -P /tmp/3SiBnGXvSN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/3SiBnGXvSN/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/3SiBnGXvSN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -Hu /tmp/3SiBnGXvSN/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -GVsnps /tmp/3SiBnGXvSN/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -GVsnps /tmp/3SiBnGXvSN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/3SiBnGXvSN/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/3SiBnGXvSN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -s ^NA00003 /tmp/3SiBnGXvSN/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -s ^NA00003 /tmp/3SiBnGXvSN/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version /tmp/3SiBnGXvSN/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -G /tmp/3SiBnGXvSN/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -G /tmp/3SiBnGXvSN/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -HG /tmp/3SiBnGXvSN/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -a /tmp/3SiBnGXvSN/many.alleles.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -a /tmp/3SiBnGXvSN/many.alleles.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -asA /tmp/3SiBnGXvSN/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -asA /tmp/3SiBnGXvSN/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -asB /tmp/3SiBnGXvSN/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -asB /tmp/3SiBnGXvSN/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -asA /tmp/3SiBnGXvSN/view.vectors.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -asA /tmp/3SiBnGXvSN/view.vectors.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i'TXT0="text"' /tmp/3SiBnGXvSN/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1/test/view.chrs.tab /tmp/3SiBnGXvSN/view.chrs.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1/test/view.chrs.tab /tmp/3SiBnGXvSN/view.chrs.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -i 'POS>=3062917' /tmp/3SiBnGXvSN/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -i 'POS>=3062917' /tmp/3SiBnGXvSN/filter.2.vcf.gz 1:3062917-3157410 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/3SiBnGXvSN/idx.1.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/3SiBnGXvSN/idx.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1/test/idx.2.bed /tmp/3SiBnGXvSN/idx.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1/test/idx.3.bed /tmp/3SiBnGXvSN/idx.3.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1/test/idx.4.bed /tmp/3SiBnGXvSN/idx.4.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -Ht 2 /tmp/3SiBnGXvSN/view-t.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -Ht 3 /tmp/3SiBnGXvSN/view-t.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/3SiBnGXvSN/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/3SiBnGXvSN/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/3SiBnGXvSN/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/3SiBnGXvSN/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/3SiBnGXvSN/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/3SiBnGXvSN/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/3SiBnGXvSN/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/3SiBnGXvSN/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/3SiBnGXvSN/overlap.vcf.gz .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.1.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.2.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.4.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.4.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.5.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -C5:nonmajor /tmp/3SiBnGXvSN/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -c6:nonmajor /tmp/3SiBnGXvSN/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -q0.3:major /tmp/3SiBnGXvSN/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/3SiBnGXvSN/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/3SiBnGXvSN/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/3SiBnGXvSN/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -a /tmp/3SiBnGXvSN/view-a.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1/test/view.sites.txt /tmp/3SiBnGXvSN/view.sites.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1/test/view.sites.txt /tmp/3SiBnGXvSN/view.sites.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1/test/view.sites.txt.gz /tmp/3SiBnGXvSN/view.sites.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1/test/view.sites.txt.gz /tmp/3SiBnGXvSN/view.sites.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -h 0 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -h 1 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -h 5 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -h 22 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -h 23 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -n 0 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -n 1 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -n 5 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -h 5 -n 5 < /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mg0 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mg0 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -G /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -G /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.4.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.cals.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/3SiBnGXvSN/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.cals.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -cv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -cv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1/test/call-G.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/call-G.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.15.1/test/call-G.2.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.15.1/test/call-G.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -m /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -m /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/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/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/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/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/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/bcftools filter -Ob -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/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/bcftools filter -Ob -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/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/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/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/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/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/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/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/bcftools filter -Ob -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/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/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/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/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/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/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/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/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/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/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/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/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -i'ALT="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/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/bcftools filter -Ob -i'ALT="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.15.1/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.15.1/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.15.1/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.15.1/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="A"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="A"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="RR"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="RR"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="RA"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="RA"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="AR"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="AR"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="AA"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="AA"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="aA"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="aA"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="HET"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="HET"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/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/bcftools filter -Ob -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/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/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools filter -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.15.1/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.15.1/test/filter.7.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/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/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/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/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.15.1/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.15.1/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.15.1/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.15.1/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/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/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/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/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/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/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.15.1/bcftools sort -m 0 /builddir/build/BUILD/bcftools-1.15.1/test/sort.vcf | /builddir/build/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/bcftools sort -Ob -m 0 /builddir/build/BUILD/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools sort -m 1000 /builddir/build/BUILD/bcftools-1.15.1/test/sort.vcf | /builddir/build/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/bcftools sort -Ob -m 1000 /builddir/build/BUILD/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/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/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.15.1/test/regions.tab /tmp/3SiBnGXvSN/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.15.1/test/regions.tab .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /builddir/build/BUILD/bcftools-1.15.1/test/regions.tab /tmp/3SiBnGXvSN/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/3SiBnGXvSN/regions.tab.gz /tmp/3SiBnGXvSN/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/3SiBnGXvSN/regions.tab.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/3SiBnGXvSN/regions.tab.gz /tmp/3SiBnGXvSN/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/3SiBnGXvSN/regions.bed /tmp/3SiBnGXvSN/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/3SiBnGXvSN/regions.bed .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/3SiBnGXvSN/regions.bed /tmp/3SiBnGXvSN/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/3SiBnGXvSN/regions.bed.gz /tmp/3SiBnGXvSN/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/3SiBnGXvSN/regions.bed.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/3SiBnGXvSN/regions.bed.gz /tmp/3SiBnGXvSN/regions.vcf.gz .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate.tab.gz -h /builddir/build/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/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate.tab.gz -h /builddir/build/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/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/3SiBnGXvSN/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/3SiBnGXvSN/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/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/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/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/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -x FORMAT /builddir/build/BUILD/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -x FORMAT /builddir/build/BUILD/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots4.vcf.gz -c +INFO /tmp/3SiBnGXvSN/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots4.vcf.gz -c +INFO /tmp/3SiBnGXvSN/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots4.tab.gz -h /builddir/build/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/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots4.tab.gz -h /builddir/build/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/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.15.1/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.15.1/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.15.1/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.15.1/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots11.vcf.gz -c FMT /tmp/3SiBnGXvSN/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots11.vcf.gz -c FMT /tmp/3SiBnGXvSN/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c FMT/newGT:=GT /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots2.vcf.gz -c FMT/newGT:=GT /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots12.vcf.gz -c FMT/GT:=newGT /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots12.vcf.gz -c FMT/GT:=newGT /tmp/3SiBnGXvSN/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.15.1/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.15.1/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -x FILTER /builddir/build/BUILD/bcftools-1.15.1/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -x FILTER /builddir/build/BUILD/bcftools-1.15.1/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/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/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/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/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/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/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/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/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/3SiBnGXvSN/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/3SiBnGXvSN/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/3SiBnGXvSN/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/3SiBnGXvSN/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate20.src.vcf.gz -c FMT/GT /tmp/3SiBnGXvSN/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate20.src.vcf.gz -c FMT/GT /tmp/3SiBnGXvSN/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate20.src.vcf.gz -c +FMT/GT /tmp/3SiBnGXvSN/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate20.src.vcf.gz -c +FMT/GT /tmp/3SiBnGXvSN/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate20.src.vcf.gz -c -FMT/GT /tmp/3SiBnGXvSN/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate20.src.vcf.gz -c -FMT/GT /tmp/3SiBnGXvSN/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/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/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/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/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.15.1/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.15.1/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate --rename-annots /builddir/build/BUILD/bcftools-1.15.1/test/annotate21.txt /builddir/build/BUILD/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob --rename-annots /builddir/build/BUILD/bcftools-1.15.1/test/annotate21.txt /builddir/build/BUILD/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/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/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/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/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/3SiBnGXvSN/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/3SiBnGXvSN/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.15.1/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.15.1/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate24.src.vcf.gz -c XX /tmp/3SiBnGXvSN/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate24.src.vcf.gz -c XX /tmp/3SiBnGXvSN/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.15.1/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.15.1/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate26.tab.gz -c CHROM,POS,~POS /builddir/build/BUILD/bcftools-1.15.1/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate26.tab.gz -c CHROM,POS,~POS /builddir/build/BUILD/bcftools-1.15.1/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/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/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/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/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots.id.vcf.gz -c ALT /tmp/3SiBnGXvSN/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots.id.vcf.gz -c ALT /tmp/3SiBnGXvSN/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/3SiBnGXvSN/annots.id.vcf.gz -c +ALT /tmp/3SiBnGXvSN/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/3SiBnGXvSN/annots.id.vcf.gz -c +ALT /tmp/3SiBnGXvSN/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/3SiBnGXvSN/checkploidy.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/3SiBnGXvSN/checkploidy.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/3SiBnGXvSN/checkploidy.2.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/3SiBnGXvSN/checkploidy.2.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/3SiBnGXvSN/checkploidy.2.vcf.gz -- -m | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/3SiBnGXvSN/checkploidy.2.bcf -- -m | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +missing2ref --no-version /tmp/3SiBnGXvSN/plugin1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +missing2ref --no-version /tmp/3SiBnGXvSN/plugin1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/plugin1.vcf.gz -- -t . -n 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/plugin1.bcf -- -t . -n 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/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/bcftools +setGT --no-version /tmp/3SiBnGXvSN/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/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/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/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/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/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.3.vcf.gz -- -t a -n pM | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.3.bcf -- -t a -n pM | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.3.vcf.gz -- -t a -n pm | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.3.bcf -- -t a -n pm | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.3.vcf.gz -- -t a -n c:1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.3.bcf -- -t a -n c:1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.3.vcf.gz -- -t a -n c:"1|1" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.3.bcf -- -t a -n c:"1|1" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.3.vcf.gz -- -t a -n c:"m|M" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.3.bcf -- -t a -n c:"m|M" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/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/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.3.bcf -- -t a -n c:0/1/1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/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/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.4.bcf -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/3SiBnGXvSN/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/bcftools +setGT --no-version /tmp/3SiBnGXvSN/setGT.4.bcf -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-AN-AC --no-version /tmp/3SiBnGXvSN/plugin1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-AN-AC --no-version /tmp/3SiBnGXvSN/plugin1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +dosage /tmp/3SiBnGXvSN/dosage.vcf.gz -- -t PL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +dosage /tmp/3SiBnGXvSN/dosage.bcf -- -t PL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +dosage /tmp/3SiBnGXvSN/dosage.vcf.gz -- -t GL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +dosage /tmp/3SiBnGXvSN/dosage.bcf -- -t GL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +dosage /tmp/3SiBnGXvSN/dosage.vcf.gz -- -t GT | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +dosage /tmp/3SiBnGXvSN/dosage.bcf -- -t GT | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixploidy --no-version /tmp/3SiBnGXvSN/fixploidy.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.15.1/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.15.1/test/fixploidy.ploidy | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixploidy --no-version /tmp/3SiBnGXvSN/fixploidy.bcf -- -s /builddir/build/BUILD/bcftools-1.15.1/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.15.1/test/fixploidy.ploidy | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +guess-ploidy /tmp/3SiBnGXvSN/view.PL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +guess-ploidy /tmp/3SiBnGXvSN/view.PL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +guess-ploidy /tmp/3SiBnGXvSN/view.GL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +guess-ploidy /tmp/3SiBnGXvSN/view.GL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/3SiBnGXvSN/view.GL.vcf.gz -- -r --gl-to-pl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/3SiBnGXvSN/view.GL.bcf -- -r --gl-to-pl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/3SiBnGXvSN/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/bcftools +tag2tag --no-version /tmp/3SiBnGXvSN/view.GP.bcf -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +add-variantkey /tmp/3SiBnGXvSN/query.variantkey.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +add-variantkey /tmp/3SiBnGXvSN/query.variantkey.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +variantkey-hex /tmp/3SiBnGXvSN/query.variantkey.vcf.gz test/ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +variantkey-hex /tmp/3SiBnGXvSN/query.variantkey.bcf test/ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +allele-length /tmp/3SiBnGXvSN/query.nucleotide.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +allele-length /tmp/3SiBnGXvSN/query.nucleotide.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/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/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/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/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/view.vcf.gz -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/view.bcf -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/view.vcf.gz -- -t AC -S /builddir/build/BUILD/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/view.bcf -- -t AC -S /builddir/build/BUILD/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/view.vcf.gz -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/view.bcf -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/many-alts.vcf.gz -- -t AN,AC | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/many-alts.bcf -- -t AN,AC | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/fill-tags-hemi.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/fill-tags-hemi.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/fill-tags-hemi.vcf.gz -- -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/fill-tags-hemi.bcf -- -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/fill-tags-hwe.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/fill-tags-hwe.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/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/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/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/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/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/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/fill-tags-AN0.bcf -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/fill-tags-VAF.vcf.gz -- -t VAF,VAF1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/fill-tags-VAF.bcf -- -t VAF,VAF1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/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/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/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/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/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/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/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/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/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/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/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/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/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/bcftools +fill-tags --no-version /tmp/3SiBnGXvSN/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/bcftools +GTisec /tmp/3SiBnGXvSN/view.vcf.gz | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.bcf | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.vcf.gz -- -H | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.bcf -- -H | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.vcf.gz -- -Hm | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.bcf -- -Hm | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.vcf.gz -- -Hmv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.bcf -- -Hmv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.vcf.gz -- -Hv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.bcf -- -Hv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.vcf.gz -- -m | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.bcf -- -m | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.vcf.gz -- -mv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.bcf -- -mv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.vcf.gz -- -v | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/3SiBnGXvSN/view.bcf -- -v | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-switch-rate /tmp/3SiBnGXvSN/trio.vcf.gz -- -p /builddir/build/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/bcftools +trio-switch-rate /tmp/3SiBnGXvSN/trio.bcf -- -p /builddir/build/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/bcftools +trio-stats /tmp/3SiBnGXvSN/trio-stats.vcf.gz -a 1 -p /builddir/build/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/bcftools +trio-stats /tmp/3SiBnGXvSN/trio-stats.bcf -a 1 -p /builddir/build/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/bcftools +trio-stats /tmp/3SiBnGXvSN/trio-stats.vcf.gz -p /builddir/build/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/bcftools +trio-stats /tmp/3SiBnGXvSN/trio-stats.bcf -p /builddir/build/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/bcftools +smpl-stats /tmp/3SiBnGXvSN/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +smpl-stats /tmp/3SiBnGXvSN/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +indel-stats /tmp/3SiBnGXvSN/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +indel-stats /tmp/3SiBnGXvSN/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +indel-stats /tmp/3SiBnGXvSN/indel-stats.vcf.gz -p /builddir/build/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/bcftools +indel-stats /tmp/3SiBnGXvSN/indel-stats.bcf -p /builddir/build/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/bcftools +indel-stats /tmp/3SiBnGXvSN/indel-stats.vcf.gz -p /builddir/build/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/bcftools +indel-stats /tmp/3SiBnGXvSN/indel-stats.bcf -p /builddir/build/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/bcftools +ad-bias /tmp/3SiBnGXvSN/ad-bias.vcf.gz -- -s /builddir/build/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/bcftools +ad-bias /tmp/3SiBnGXvSN/ad-bias.bcf -- -s /builddir/build/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/bcftools +ad-bias /tmp/3SiBnGXvSN/ad-bias.2.vcf.gz -- -s /builddir/build/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/bcftools +ad-bias /tmp/3SiBnGXvSN/ad-bias.2.bcf -- -s /builddir/build/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/bcftools +ad-bias /tmp/3SiBnGXvSN/ad-bias.vcf.gz --no-version -- -s /builddir/build/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/bcftools +ad-bias /tmp/3SiBnGXvSN/ad-bias.bcf --no-version -- -s /builddir/build/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/bcftools +ad-bias /tmp/3SiBnGXvSN/ad-bias.2.vcf.gz --no-version -- -s /builddir/build/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/bcftools +ad-bias /tmp/3SiBnGXvSN/ad-bias.2.bcf --no-version -- -s /builddir/build/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/bcftools +af-dist /tmp/3SiBnGXvSN/af-dist.vcf.gz | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +af-dist /tmp/3SiBnGXvSN/af-dist.bcf | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/3SiBnGXvSN/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -i /tmp/3SiBnGXvSN/fixref.2b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/3SiBnGXvSN/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -i /tmp/3SiBnGXvSN/fixref.2b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/3SiBnGXvSN/fixref.3.vcf.gz -- -f /builddir/build/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/bcftools +fixref /tmp/3SiBnGXvSN/fixref.3.bcf -- -f /builddir/build/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/bcftools +fixref /tmp/3SiBnGXvSN/fixref.2a.vcf.gz -- -f /builddir/build/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/bcftools +fixref /tmp/3SiBnGXvSN/fixref.2a.bcf -- -f /builddir/build/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/bcftools +fixref /tmp/3SiBnGXvSN/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -m flip | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/3SiBnGXvSN/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -m flip | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/3SiBnGXvSN/fixref.2a.vcf.gz -- -f /builddir/build/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/bcftools +fixref /tmp/3SiBnGXvSN/fixref.2a.bcf -- -f /builddir/build/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/bcftools +fill-from-fasta /tmp/3SiBnGXvSN/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1/test/aa.fa -c AA -h /builddir/build/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/bcftools +fill-from-fasta /tmp/3SiBnGXvSN/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1/test/aa.fa -c AA -h /builddir/build/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/bcftools +fill-from-fasta /tmp/3SiBnGXvSN/aa.vcf.gz -- -f /builddir/build/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/bcftools +fill-from-fasta /tmp/3SiBnGXvSN/aa.bcf -- -f /builddir/build/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/bcftools +fill-from-fasta /tmp/3SiBnGXvSN/ref.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -c REF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/3SiBnGXvSN/ref.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -c REF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/3SiBnGXvSN/view.vcf.gz -- -s NA00001 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/3SiBnGXvSN/view.bcf -- -s NA00001 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/3SiBnGXvSN/view.vcf.gz -- -s NA00001,NA00002 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/3SiBnGXvSN/view.bcf -- -s NA00001,NA00002 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/3SiBnGXvSN/view.vcf.gz -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/3SiBnGXvSN/view.bcf -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/3SiBnGXvSN/mendelian.vcf.gz -t mom1,dad1,child1 -md | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/3SiBnGXvSN/mendelian.bcf -t mom1,dad1,child1 -md | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/3SiBnGXvSN/mendelian.vcf.gz -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/3SiBnGXvSN/mendelian.bcf -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/3SiBnGXvSN/mendelian.vcf.gz -t mom1,dad1,child1 -mx | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/3SiBnGXvSN/mendelian.bcf -t mom1,dad1,child1 -mx | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/3SiBnGXvSN/mendelian.vcf.gz -t mom1,dad1,child1 -ma | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/3SiBnGXvSN/mendelian.bcf -t mom1,dad1,child1 -ma | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/3SiBnGXvSN/mendelian.vcf.gz -t mom1,dad1,child1 -mu | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/3SiBnGXvSN/mendelian.bcf -t mom1,dad1,child1 -mu | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/3SiBnGXvSN/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/bcftools +contrast /tmp/3SiBnGXvSN/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/bcftools +contrast /tmp/3SiBnGXvSN/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.15.1/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.15.1/test/contrast1.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/3SiBnGXvSN/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.15.1/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.15.1/test/contrast1.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/3SiBnGXvSN/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/bcftools +contrast /tmp/3SiBnGXvSN/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/bcftools +contrast /tmp/3SiBnGXvSN/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/bcftools +contrast /tmp/3SiBnGXvSN/contrast.1.bcf -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/3SiBnGXvSN/contrast.1.vcf.gz -a NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/3SiBnGXvSN/contrast.1.bcf -a NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.1.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.1.bcf -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/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/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.2.bcf -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.4.bcf -p proband,father,mother | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.8.vcf.gz -p proband,father,mother | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.8.bcf -p proband,father,mother | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.9.vcf.gz -p 1X:proband,father,mother --use-NAIVE | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.9.bcf -p 1X:proband,father,mother --use-NAIVE | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.9.vcf.gz -p 2X:proband,father,mother --use-NAIVE | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.9.bcf -p 2X:proband,father,mother --use-NAIVE | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.10.vcf.gz -p proband,father,mother --with-pAD | /builddir/build/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/bcftools +trio-dnm2 /tmp/3SiBnGXvSN/trio-dnm/trio-dnm.10.bcf -p proband,father,mother --with-pAD | /builddir/build/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/bcftools +gvcfz /tmp/3SiBnGXvSN/gvcfz.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/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/bcftools +gvcfz /tmp/3SiBnGXvSN/gvcfz.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/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/bcftools +gvcfz /tmp/3SiBnGXvSN/gvcfz.vcf.gz -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/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/bcftools +gvcfz /tmp/3SiBnGXvSN/gvcfz.bcf -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/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/bcftools +gvcfz /tmp/3SiBnGXvSN/gvcfz.2.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/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/bcftools +gvcfz /tmp/3SiBnGXvSN/gvcfz.2.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/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/bcftools +remove-overlaps /tmp/3SiBnGXvSN/remove-overlaps.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +remove-overlaps /tmp/3SiBnGXvSN/remove-overlaps.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +remove-overlaps /tmp/3SiBnGXvSN/remove-overlaps.vcf.gz -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +remove-overlaps /tmp/3SiBnGXvSN/remove-overlaps.bcf -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/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/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/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/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/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/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.vcf.gz -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.bcf -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.vcf.gz -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/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/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.bcf -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/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/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.vcf.gz -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/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/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.bcf -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/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/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.5.vcf.gz -s :synonymous -c Consequence | /builddir/build/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/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.5.bcf -s :synonymous -c Consequence | /builddir/build/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/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.5.vcf.gz -s :synonymous -x -c Consequence | /builddir/build/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/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.5.bcf -s :synonymous -x -c Consequence | /builddir/build/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.6.vcf.gz -c - | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.6.bcf -c - | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.6.vcf.gz -c - -s worst | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/3SiBnGXvSN/split-vep.6.bcf -c - -s worst | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +split-vep /tmp/3SiBnGXvSN/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/bcftools +parental-origin /tmp/3SiBnGXvSN/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/bcftools +parental-origin /tmp/3SiBnGXvSN/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/bcftools +parental-origin /tmp/3SiBnGXvSN/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/bcftools +parental-origin /tmp/3SiBnGXvSN/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/bcftools +parental-origin /tmp/3SiBnGXvSN/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/bcftools +parental-origin /tmp/3SiBnGXvSN/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/bcftools +parental-origin /tmp/3SiBnGXvSN/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/bcftools +parental-origin /tmp/3SiBnGXvSN/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/bcftools +parental-origin /tmp/3SiBnGXvSN/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/bcftools +parental-origin /tmp/3SiBnGXvSN/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/bcftools +prune -w 1 -a r2,LD,HD /tmp/3SiBnGXvSN/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/3SiBnGXvSN/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/3SiBnGXvSN/prune.2.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/3SiBnGXvSN/prune.2.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/3SiBnGXvSN/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/3SiBnGXvSN/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/3SiBnGXvSN/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/3SiBnGXvSN/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/3SiBnGXvSN/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/3SiBnGXvSN/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/3SiBnGXvSN/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/3SiBnGXvSN/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N 1st /tmp/3SiBnGXvSN/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N 1st /tmp/3SiBnGXvSN/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/3SiBnGXvSN/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/3SiBnGXvSN/prune.1.bcf | grep -v ^##bcftools_ .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/3SiBnGXvSN/split.1.1 && cd /tmp/3SiBnGXvSN/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/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/3SiBnGXvSN/split.1.2 -S /builddir/build/BUILD/bcftools-1.15.1/test/split.smpl.1.2.txt && cd /tmp/3SiBnGXvSN/split.1.2 && for f in A.vcf B.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/3SiBnGXvSN/split.1.3 -S /builddir/build/BUILD/bcftools-1.15.1/test/split.smpl.1.3.txt && cd /tmp/3SiBnGXvSN/split.1.3 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/3SiBnGXvSN/split.1.4 -S /builddir/build/BUILD/bcftools-1.15.1/test/split.smpl.1.3.txt -i 'GT[0]="alt"' && cd /tmp/3SiBnGXvSN/split.1.4 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/3SiBnGXvSN/split.1.5 -S /builddir/build/BUILD/bcftools-1.15.1/test/split.smpl.1.3.txt -i 'GT="alt"' && cd /tmp/3SiBnGXvSN/split.1.5 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/3SiBnGXvSN/split.1.6 -S /builddir/build/BUILD/bcftools-1.15.1/test/split.smpl.1.4.txt -i 'GT="alt"' && cd /tmp/3SiBnGXvSN/split.1.6 && for f in file1.vcf file2.vcf file3.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/3SiBnGXvSN/split.1.7 -G /builddir/build/BUILD/bcftools-1.15.1/test/split.grp.1.1.txt && cd /tmp/3SiBnGXvSN/split.1.7 && for f in A.vcf A1.vcf A2.vcf B.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.2.vcf -o /tmp/3SiBnGXvSN/split.2.1 && cd /tmp/3SiBnGXvSN/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/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/3SiBnGXvSN/scatter.1.1 -n 3 && cd /tmp/3SiBnGXvSN/scatter.1.1 && cat 0.vcf 1.vcf 2.vcf | grep -v ^## .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/3SiBnGXvSN/scatter.1.2 -s 21,22 && cd /tmp/3SiBnGXvSN/scatter.1.2 && cat 21.vcf 22.vcf | grep -v ^## .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/3SiBnGXvSN/scatter.1.3 -s 21,22 -x X && cd /tmp/3SiBnGXvSN/scatter.1.3 && cat 21.vcf 22.vcf X.vcf | grep -v ^## .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version /tmp/3SiBnGXvSN/concat.1.a.vcf.gz /tmp/3SiBnGXvSN/concat.1.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob /tmp/3SiBnGXvSN/concat.1.a.vcf.gz /tmp/3SiBnGXvSN/concat.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version /tmp/3SiBnGXvSN/concat.1.a.bcf /tmp/3SiBnGXvSN/concat.1.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob /tmp/3SiBnGXvSN/concat.1.a.bcf /tmp/3SiBnGXvSN/concat.1.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -a /tmp/3SiBnGXvSN/concat.2.a.vcf.gz /tmp/3SiBnGXvSN/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -a /tmp/3SiBnGXvSN/concat.2.a.vcf.gz /tmp/3SiBnGXvSN/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -a /tmp/3SiBnGXvSN/concat.2.a.bcf /tmp/3SiBnGXvSN/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -a /tmp/3SiBnGXvSN/concat.2.a.bcf /tmp/3SiBnGXvSN/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -aD /tmp/3SiBnGXvSN/concat.2.a.vcf.gz /tmp/3SiBnGXvSN/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -aD /tmp/3SiBnGXvSN/concat.2.a.vcf.gz /tmp/3SiBnGXvSN/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -aD /tmp/3SiBnGXvSN/concat.2.a.bcf /tmp/3SiBnGXvSN/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -aD /tmp/3SiBnGXvSN/concat.2.a.bcf /tmp/3SiBnGXvSN/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/3SiBnGXvSN/concat.3.a.vcf.gz /tmp/3SiBnGXvSN/concat.3.b.vcf.gz /tmp/3SiBnGXvSN/concat.3.0.vcf.gz /tmp/3SiBnGXvSN/concat.3.c.vcf.gz /tmp/3SiBnGXvSN/concat.3.d.vcf.gz /tmp/3SiBnGXvSN/concat.3.e.vcf.gz /tmp/3SiBnGXvSN/concat.3.f.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/3SiBnGXvSN/concat.3.a.vcf.gz /tmp/3SiBnGXvSN/concat.3.b.vcf.gz /tmp/3SiBnGXvSN/concat.3.0.vcf.gz /tmp/3SiBnGXvSN/concat.3.c.vcf.gz /tmp/3SiBnGXvSN/concat.3.d.vcf.gz /tmp/3SiBnGXvSN/concat.3.e.vcf.gz /tmp/3SiBnGXvSN/concat.3.f.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/3SiBnGXvSN/concat.3.a.bcf /tmp/3SiBnGXvSN/concat.3.b.bcf /tmp/3SiBnGXvSN/concat.3.0.bcf /tmp/3SiBnGXvSN/concat.3.c.bcf /tmp/3SiBnGXvSN/concat.3.d.bcf /tmp/3SiBnGXvSN/concat.3.e.bcf /tmp/3SiBnGXvSN/concat.3.f.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/3SiBnGXvSN/concat.3.a.bcf /tmp/3SiBnGXvSN/concat.3.b.bcf /tmp/3SiBnGXvSN/concat.3.0.bcf /tmp/3SiBnGXvSN/concat.3.c.bcf /tmp/3SiBnGXvSN/concat.3.d.bcf /tmp/3SiBnGXvSN/concat.3.e.bcf /tmp/3SiBnGXvSN/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 3678213440 .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --naive-force /tmp/3SiBnGXvSN/naive_concat.0.bcf /tmp/3SiBnGXvSN/naive_concat.1.bcf /tmp/3SiBnGXvSN/naive_concat.2.bcf /tmp/3SiBnGXvSN/naive_concat.3.bcf /tmp/3SiBnGXvSN/naive_concat.4.bcf /tmp/3SiBnGXvSN/naive_concat.5.bcf /tmp/3SiBnGXvSN/naive_concat.6.bcf /tmp/3SiBnGXvSN/naive_concat.7.bcf /tmp/3SiBnGXvSN/naive_concat.8.bcf /tmp/3SiBnGXvSN/naive_concat.9.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --naive /tmp/3SiBnGXvSN/naive_concat.0.vcf.gz /tmp/3SiBnGXvSN/naive_concat.1.vcf.gz /tmp/3SiBnGXvSN/naive_concat.2.vcf.gz /tmp/3SiBnGXvSN/naive_concat.3.vcf.gz /tmp/3SiBnGXvSN/naive_concat.4.vcf.gz /tmp/3SiBnGXvSN/naive_concat.5.vcf.gz /tmp/3SiBnGXvSN/naive_concat.6.vcf.gz /tmp/3SiBnGXvSN/naive_concat.7.vcf.gz /tmp/3SiBnGXvSN/naive_concat.8.vcf.gz /tmp/3SiBnGXvSN/naive_concat.9.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l /tmp/3SiBnGXvSN/concat.4.a.vcf.gz /tmp/3SiBnGXvSN/concat.4.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l /tmp/3SiBnGXvSN/concat.4.a.vcf.gz /tmp/3SiBnGXvSN/concat.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l /tmp/3SiBnGXvSN/concat.4.a.bcf /tmp/3SiBnGXvSN/concat.4.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l /tmp/3SiBnGXvSN/concat.4.a.bcf /tmp/3SiBnGXvSN/concat.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/3SiBnGXvSN/concat.5.a.vcf.gz /tmp/3SiBnGXvSN/concat.5.b.vcf.gz /tmp/3SiBnGXvSN/concat.5.c.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/3SiBnGXvSN/concat.5.a.vcf.gz /tmp/3SiBnGXvSN/concat.5.b.vcf.gz /tmp/3SiBnGXvSN/concat.5.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/3SiBnGXvSN/concat.5.a.bcf /tmp/3SiBnGXvSN/concat.5.b.bcf /tmp/3SiBnGXvSN/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/3SiBnGXvSN/concat.5.a.bcf /tmp/3SiBnGXvSN/concat.5.b.bcf /tmp/3SiBnGXvSN/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l --ligate-force /tmp/3SiBnGXvSN/concat.5.a.bcf /tmp/3SiBnGXvSN/concat.5.b.bcf /tmp/3SiBnGXvSN/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l --ligate-force /tmp/3SiBnGXvSN/concat.5.a.bcf /tmp/3SiBnGXvSN/concat.5.b.bcf /tmp/3SiBnGXvSN/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.hdr /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.hdr /tmp/3SiBnGXvSN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3SiBnGXvSN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.hdr /tmp/3SiBnGXvSN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3SiBnGXvSN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples /tmp/3SiBnGXvSN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3SiBnGXvSN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples /tmp/3SiBnGXvSN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3SiBnGXvSN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples2 /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples2 /tmp/3SiBnGXvSN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3SiBnGXvSN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples2 /tmp/3SiBnGXvSN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3SiBnGXvSN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples3 /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples3 /tmp/3SiBnGXvSN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3SiBnGXvSN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples3 /tmp/3SiBnGXvSN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3SiBnGXvSN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples4 /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples4 /tmp/3SiBnGXvSN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3SiBnGXvSN/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples4 /tmp/3SiBnGXvSN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3SiBnGXvSN/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.empty.hdr /builddir/build/BUILD/bcftools-1.15.1/test/empty.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1/test/empty.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.empty.hdr /tmp/3SiBnGXvSN/empty.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3SiBnGXvSN/empty.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.empty.hdr /tmp/3SiBnGXvSN/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3SiBnGXvSN/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1/test/reheader.fai /builddir/build/BUILD/bcftools-1.15.1/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1/test/reheader.fai /tmp/3SiBnGXvSN/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1/test/reheader.fai /tmp/3SiBnGXvSN/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1/test/reheader.fai /builddir/build/BUILD/bcftools-1.15.1/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1/test/reheader.fai /tmp/3SiBnGXvSN/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1/test/reheader.fai /tmp/3SiBnGXvSN/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/3SiBnGXvSN/rename.map -Ov /tmp/3SiBnGXvSN/annotate.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/3SiBnGXvSN/rename.map -Ob /tmp/3SiBnGXvSN/annotate.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/3SiBnGXvSN/rename.map -Ov /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/3SiBnGXvSN/rename.map -Ob /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. /tmp/3SiBnGXvSN/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids /tmp/3SiBnGXvSN/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids --3N6 /tmp/3SiBnGXvSN/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- /tmp/3SiBnGXvSN/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --tag PL /tmp/3SiBnGXvSN/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --tag PL /tmp/3SiBnGXvSN/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids /tmp/3SiBnGXvSN/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --vcf-ids /tmp/3SiBnGXvSN/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --3N6 /tmp/3SiBnGXvSN/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --3N6 /tmp/3SiBnGXvSN/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --3N6 --vcf-ids /tmp/3SiBnGXvSN/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --3N6 --vcf-ids /tmp/3SiBnGXvSN/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h -,.,. /tmp/3SiBnGXvSN/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h -,.,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h .,-,. /tmp/3SiBnGXvSN/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h .,-,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h .,-,. --vcf-ids /tmp/3SiBnGXvSN/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h .,.,- /tmp/3SiBnGXvSN/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -H /builddir/build/BUILD/bcftools-1.15.1/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -H /builddir/build/BUILD/bcftools-1.15.1/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hls.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --haplegendsample -,.,. /tmp/3SiBnGXvSN/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.hap-missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample -,. /tmp/3SiBnGXvSN/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample -,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample -,. --vcf-ids /tmp/3SiBnGXvSN/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample .,- /tmp/3SiBnGXvSN/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/3SiBnGXvSN/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/3SiBnGXvSN/convert.gvcf.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.15.1/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.15.1/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.15.1/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.15.1/test/convert.23andme | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab -c /tmp/3SiBnGXvSN/consensus.1.chain.new >/dev/null; cat /tmp/3SiBnGXvSN/consensus.1.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab -c /tmp/3SiBnGXvSN/consensus.2.chain.new >/dev/null; cat /tmp/3SiBnGXvSN/consensus.2.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab --mask-with X -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab -c /tmp/3SiBnGXvSN/consensus.3.chain.new >/dev/null; cat /tmp/3SiBnGXvSN/consensus.3.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -H 1 -c /tmp/3SiBnGXvSN/consensus.4.chain.new >/dev/null; cat /tmp/3SiBnGXvSN/consensus.4.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/empty.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus4.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus2.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus5.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus6.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus6.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -a . .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus8.vcf.gz -f /builddir/build/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/bcftools consensus /tmp/3SiBnGXvSN/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -a . -i 'ALT!=""' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -a . -e 'MinDP>15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -a . -e 'MinDP<15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.12.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.13.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.13.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.14.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.14.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.12.vcf.gz -f /builddir/build/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/bcftools consensus /tmp/3SiBnGXvSN/consensus.15.vcf.gz -f /builddir/build/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/bcftools consensus /tmp/3SiBnGXvSN/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -I .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -H I .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.17.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus2.fa -M N -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.17.bed .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.18.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.18.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/3SiBnGXvSN/consensus.19.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.19.fa .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/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/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -b /tmp/3SiBnGXvSN/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob -b /tmp/3SiBnGXvSN/mpileup.bam.urllist | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/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/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -b /tmp/3SiBnGXvSN/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob -b /tmp/3SiBnGXvSN/mpileup.cram.urllist | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/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/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/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/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/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/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/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/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/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/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/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/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/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/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/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/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/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/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/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/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/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/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/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/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/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/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/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/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/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/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/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/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/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/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/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/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/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/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/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/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/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/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/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/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/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/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/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/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/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/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/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/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/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/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/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/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/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/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/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/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/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/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/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/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/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/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/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/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/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/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/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/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/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/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/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/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/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/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/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/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/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/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/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/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/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/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/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/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/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/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/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/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/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/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/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/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/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/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/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/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/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/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/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/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/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/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/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/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/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/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/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/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/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/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/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/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/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/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/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/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/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/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/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/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/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/test/mpileup/mpileup-SCR.fa /builddir/build/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/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/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/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/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/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/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/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq.gff3 /builddir/build/BUILD/bcftools-1.15.1/test/csq.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq.chr.gff3 /builddir/build/BUILD/bcftools-1.15.1/test/csq.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq.2.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq.2.vcf | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq.2.gff --ncsq 64 /builddir/build/BUILD/bcftools-1.15.1/test/csq.2.vcf | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000624631/ENST00000624631.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000624631/ENST00000624631.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000624631/ambiguous.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000593942/ENST00000593942.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000593942/ENST00000593942.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000593942/last-codon-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/test/csq/ENST00000580206 && /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000557788/ENST00000557788.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000557788/ENST00000557788.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000557788/long-overlap-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000545279/ENST00000545279.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000545279/ENST00000545279.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000545279/splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000528237/ENST00000528237.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000528237/ENST00000528237.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520868/ENST00000520868.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520868/ENST00000520868.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520868/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000519442/ENST00000519442.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000519442/ENST00000519442.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000519442/synon-splice-region-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000518414/ENST00000518414.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000518414/ENST00000518414.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000448695/ENST00000448695.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000448695/ENST00000448695.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000436063/ENST00000436063.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000436063/ENST00000436063.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000436063/insert-before-utr.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/test/csq/ENST00000422159 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /builddir/build/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/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420670/start-stop-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420670/segfault.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420190/ENST00000420190.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420190/ENST00000420190.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420190/abort-in-csq-push.vcf | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000413103/ENST00000413103.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000413103/ENST00000413103.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000413103/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000410009/ENST00000410009.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000410009/ENST00000410009.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000410009/frameshift.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/test/csq/ENST00000410009 && /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000409523/ENST00000409523.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000409523/ENST00000409523.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000409523/long-overlapping-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000400151/ENST00000400151.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000400151/ENST00000400151.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000400151/long-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000390520/ENST00000390520.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000390520/ENST00000390520.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000390520/deletion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000382647/ENST00000382647.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000382647/ENST00000382647.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000381157/ENST00000381157.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000381157/ENST00000381157.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000381157/haploid-diploid.vcf | /builddir/build/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/test/csq/ENST00000379416 && /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000375992/ENST00000375992.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000375992/ENST00000375992.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000368801/ENST00000368801.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000368801/ENST00000368801.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000368801/compound-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000368801.2/ENST00000368801.2.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000368801.2/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000357367/ENST00000357367.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000357367/ENST00000357367.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000357367/stop-retained.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249.2/ENST00000318249.2.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000301246/ENST00000301246.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000301246/ENST00000301246.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000301246/15bp-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000285021/ENST00000285021.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000285021/ENST00000285021.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000271583/ENST00000271583.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000271583/ENST00000271583.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000271583/splice-acceptor.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000269081/ENST00000269081.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000269081/ENST00000269081.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000263103-INS/insertions.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000256452/ENST00000256452.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000256452/ENST00000256452.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000256452/intron.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000230048/ENST00000230048.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000230048/ENST00000230048.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000230048/start-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000227471/ENST00000227471.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000227471/ENST00000227471.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/start-lost-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/test/csq/ENST00000000000 && /builddir/build/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/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/test/csq/ENSMUST00000133836 && /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/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/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENSG00000173376/ENSG00000173376.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENSG00000173376/ENSG00000173376.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENSG00000173376/synon.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /builddir/build/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/test/csq/EMN908947 && /builddir/build/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/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0003/EDUMMY0003.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0003/EDUMMY0003.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0003/long-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0002/EDUMMY0002.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0002/EDUMMY0002.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0002/boundaries.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/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/bcftools roh /builddir/build/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/bcftools roh /builddir/build/BUILD/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.15.1/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.15.1/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1/bcftools roh /builddir/build/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/bcftools roh /builddir/build/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/bcftools roh /builddir/build/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/bcftools roh /builddir/build/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/bcftools gtcheck -e 0 /tmp/3SiBnGXvSN/gtcheck.1.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,GT /tmp/3SiBnGXvSN/gtcheck.1.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,PL /tmp/3SiBnGXvSN/gtcheck.1.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,GT /tmp/3SiBnGXvSN/gtcheck.1.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,PL /tmp/3SiBnGXvSN/gtcheck.1.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -p s1,s1 /tmp/3SiBnGXvSN/gtcheck.1.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/3SiBnGXvSN/gtcheck.2.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/3SiBnGXvSN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/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/3SiBnGXvSN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1/test/gtcheck.3.pairs /tmp/3SiBnGXvSN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL /tmp/3SiBnGXvSN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 --n-matches 4 /tmp/3SiBnGXvSN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/3SiBnGXvSN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/3SiBnGXvSN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/3SiBnGXvSN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/3SiBnGXvSN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/3SiBnGXvSN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -p B,C,B,D /tmp/3SiBnGXvSN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,GT -H /tmp/3SiBnGXvSN/gtcheck.1.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,PL -H /tmp/3SiBnGXvSN/gtcheck.1.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,GT -H /tmp/3SiBnGXvSN/gtcheck.1.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,PL -H /tmp/3SiBnGXvSN/gtcheck.1.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/3SiBnGXvSN/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/3SiBnGXvSN/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -u GT -e 30 /tmp/3SiBnGXvSN/gtcheck.1.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/3SiBnGXvSN/gtcheck.1.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -u GT -e 300 /tmp/3SiBnGXvSN/gtcheck.1.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -u PL -e 30 /tmp/3SiBnGXvSN/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck /tmp/3SiBnGXvSN/gtcheck.ntop.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck --n-matches 2 /tmp/3SiBnGXvSN/gtcheck.ntop.vcf.gz -g /tmp/3SiBnGXvSN/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck /tmp/3SiBnGXvSN/gtcheck.5.vcf.gz -g /tmp/3SiBnGXvSN/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-1.15.1-2.fc38.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.xtkVbN + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.15.1 + DOCDIR=/builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/share/doc/bcftools + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/share/doc/bcftools + cp -pr AUTHORS /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/share/doc/bcftools + cp -pr NEWS /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/share/doc/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.84FGZc + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.15.1 + LICENSEDIR=/builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/share/licenses/bcftools + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/share/licenses/bcftools + cp -pr LICENSE /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64/usr/share/licenses/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Provides: bcftools = 1.15.1-2.fc38 bcftools(x86-64) = 1.15.1-2.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl /usr/bin/python3 libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libgsl.so.27()(64bit) libgslcblas.so.0()(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libperl.so.5.36()(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Conflicts: samtools < 1.0 Processing files: bcftools-debugsource-1.15.1-2.fc38.x86_64 Provides: bcftools-debugsource = 1.15.1-2.fc38 bcftools-debugsource(x86-64) = 1.15.1-2.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bcftools-debuginfo-1.15.1-2.fc38.x86_64 Provides: bcftools-debuginfo = 1.15.1-2.fc38 bcftools-debuginfo(x86-64) = 1.15.1-2.fc38 debuginfo(build-id) = 02c8aefd7597c1fab4d9465cf4dfc88eedc4378f debuginfo(build-id) = 109572e4f6dccf51de1c1eb46c5ed997ab77373f debuginfo(build-id) = 12d171a99022d027abaf50ef89529651be145e62 debuginfo(build-id) = 169bfaec82ba5f3a07caca6c88c5910745b9f80b debuginfo(build-id) = 172b413efee3b79288f9302aa397ca599e2ffd7b debuginfo(build-id) = 1f6458b409155c1f75c5d30796e190189138efaf debuginfo(build-id) = 24ebd80827ce730d1b4b7d95d4dd801f01634162 debuginfo(build-id) = 26306cebf54b6bef2542f53594119b0773a5e345 debuginfo(build-id) = 27cde8e32106bb141c7d8507313fa4b85fafde7d debuginfo(build-id) = 3549f07921725ef6dec05a4ecfde4a070d37049a debuginfo(build-id) = 367eaabb5111055c0d67d75930fc1c7b0af8f170 debuginfo(build-id) = 36b6f41d904f185fcda03c530ff50259573a8633 debuginfo(build-id) = 55a405f6e368fdb5d00d6459b70fdaf455dd6451 debuginfo(build-id) = 59e942b45e755c718b1ad26d39b32f9c7a2586ee debuginfo(build-id) = 5a5a38e633bdb04ba1e5bdbc56a09069bd1255ed debuginfo(build-id) = 5c877d61fc175b54d3e97393387ba8ecd1daf442 debuginfo(build-id) = 6ffa2a27538ee037635577314c10a49c4a0559d4 debuginfo(build-id) = 72fdda99ca00eecf2e23cadebcc166fb0e1ae27c debuginfo(build-id) = 79d8a7e2f8355ab70b33b2b04bedac7dc7a42a76 debuginfo(build-id) = 7cd1a6a9bb56b083bc3e2e46ffcd70a885cb6831 debuginfo(build-id) = 7df037686edb7eb46a1e66855db482635f98af65 debuginfo(build-id) = 7fd33140eccab5da40e7ab39f8712d0a502dd47a debuginfo(build-id) = 80561920bdf3597fa4b61639421b8fb2d6fbb588 debuginfo(build-id) = 90411365020d3e7e4d07df70fba03ff54dc54b38 debuginfo(build-id) = 91d92d73d1061e7a085e6079f55567024bd773b0 debuginfo(build-id) = a7fce0cb41980503dcebe3c67155947bbfbd4ec3 debuginfo(build-id) = a8948723f08d837da511946470ddb2ffcc414444 debuginfo(build-id) = adfa3b721a4ae8ffaf53e654ab887561daecdb77 debuginfo(build-id) = b17ffe4d25df70f436c4b10d152e6e8a63e4cfec debuginfo(build-id) = b1db421ebf2a8238723e34b9bf5b7010288ab465 debuginfo(build-id) = b680c32626b048cb405757c34516db182a801e55 debuginfo(build-id) = baee3aaed156e48f671f6dbf9ec32725496ba290 debuginfo(build-id) = bee8d2c0e09f8a24d5b8c041e764736b130b272c debuginfo(build-id) = c15d43d9e5a02b8595a154524d93c488c0138451 debuginfo(build-id) = e70e8d082f94aa3c2f965c63825f13500a4f9426 debuginfo(build-id) = ed3c8dcc081c049ff0fc08e79fd6004363c013e3 debuginfo(build-id) = f133a5d5bf23425e63c3ccc660755a4f2e6b34a2 debuginfo(build-id) = f4351f1eaed80771d67ac913afcc6aeeca4b7208 debuginfo(build-id) = fa26929b25f49248f4076af1ea0cb6e284c6e185 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bcftools-debugsource(x86-64) = 1.15.1-2.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64 Wrote: /builddir/build/RPMS/bcftools-debugsource-1.15.1-2.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.15.1-2.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/bcftools-1.15.1-2.fc38.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.hxDura + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.15.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.jungSm + umask 022 + cd /builddir/build/BUILD + rm -rf bcftools-1.15.1 bcftools-1.15.1.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild bcftools-1.15.1-2.fc38.src.rpm Finish: build phase for bcftools-1.15.1-2.fc38.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1671795578.114598/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1671795578.114598/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1671795578.114598/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/bcftools-1.15.1-2.fc38.src.rpm) Config(child) 1 minutes 49 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