Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c199' (ECDSA) to the list of known hosts. Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 2447053 --chroot fedora-rawhide-i386 --detached Version: 0.52 Task: {'appstream': True, 'background': False, 'bootstrap': 'off', 'build_id': 2447053, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-i386', 'enable_net': False, 'fedora_review': False, 'git_hash': 'bd743066f5be67c7ee23b528c6807f641b2058db', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jaruga/staging/bcftools.git', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'bcftools', 'package_version': '1.13-1.fc35', 'project_dirname': 'staging', 'project_name': 'staging', 'project_owner': 'jaruga', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jaruga/staging/fedora-rawhide-i386/', 'id': 'copr_base', 'name': 'Copr repository'}], 'sandbox': 'jaruga/staging--jaruga', 'source_json': {}, 'source_type': None, 'submitter': 'jaruga', 'task_id': '2447053-fedora-rawhide-i386', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jaruga/staging/bcftools.git /var/lib/copr-rpmbuild/workspace/workdir-nytxz3sl/bcftools --depth 500 --no-single-branch cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jaruga/staging/bcftools.git', '/var/lib/copr-rpmbuild/workspace/workdir-nytxz3sl/bcftools', '--depth', '500', '--no-single-branch'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-nytxz3sl/bcftools'... Running: git checkout bd743066f5be67c7ee23b528c6807f641b2058db cmd: ['git', 'checkout', 'bd743066f5be67c7ee23b528c6807f641b2058db'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-nytxz3sl/bcftools rc: 0 stdout: stderr: Note: switching to 'bd743066f5be67c7ee23b528c6807f641b2058db'. 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 bd74306 automatic import of bcftools Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-nytxz3sl/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-1.13.tar.bz2 INFO: Calling: curl -H Pragma: -o bcftools-1.13.tar.bz2 --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jaruga/staging/bcftools/bcftools-1.13.tar.bz2/md5/c540ca90d61b7bb395f52aafc959fd4a/bcftools-1.13.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 6744k 100 6744k 0 0 40.1M 0 --:--:-- --:--:-- --:--:-- 40.1M INFO: Reading stdout from command: md5sum bcftools-1.13.tar.bz2 /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-nytxz3sl/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-nytxz3sl/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1628447957.888446 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 2.12 starting (python version = 3.9.4, NVR = mock-2.12-1.fc34)... 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-nytxz3sl/bcftools/bcftools.spec) Config(fedora-rawhide-i686) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-1628447957.888446/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: 2.12 INFO: Mock Version: 2.12 Start: dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 33 kB/s | 8.3 kB 00:00 local 27 MB/s | 57 MB 00:02 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: [1mbash [m i686 5.1.8-2.fc35 local 1.7 M [1mbzip2 [m i686 1.0.8-9.fc35 local 52 k [1mcoreutils [m i686 8.32-31.fc35 local 1.2 M [1mcpio [m i686 2.13-11.fc35 local 274 k [1mdiffutils [m i686 3.8-1.fc35 local 410 k [1mfedora-release [m noarch 35-0.14 local 11 k [1mfindutils [m i686 1:4.8.0-4.fc35 local 548 k [1mgawk [m i686 5.1.0-4.fc35 local 988 k [1mglibc-minimal-langpack [m i686 2.34-1.fc35 local 141 k [1mgrep [m i686 3.6-4.fc35 local 262 k [1mgzip [m i686 1.10-5.fc35 local 148 k [1minfo [m i686 6.8-2.fc35 local 228 k [1mpatch [m i686 2.7.6-15.fc35 local 146 k [1mredhat-rpm-config [m noarch 194-1.fc35 local 64 k [1mrpm-build [m i686 4.17.0-0.beta1.0.fc35.2 local 61 k [1msed [m i686 4.8-8.fc35 local 299 k [1mshadow-utils [m i686 2:4.9-1.fc35 local 1.1 M [1mtar [m i686 2:1.34-2.fc35 local 897 k [1munzip [m i686 6.0-53.fc35 local 179 k [1mutil-linux [m i686 2.37-6.fc35 local 2.2 M [1mwhich [m i686 2.21-27.fc35 local 41 k [1mxz [m i686 5.2.5-7.fc35 local 219 k Installing dependencies: [1malternatives [m i686 1.19-1.fc35 local 36 k [1maudit-libs [m i686 3.0.4-1.fc35 local 121 k [1mbasesystem [m noarch 11-12.fc35 local 7.0 k [1mbinutils [m i686 2.37-3.fc35 local 6.0 M [1mbinutils-gold [m i686 2.37-3.fc35 local 806 k [1mbzip2-libs [m i686 1.0.8-9.fc35 local 40 k [1mca-certificates [m noarch 2021.2.50-3.fc35 local 352 k [1mcoreutils-common [m i686 8.32-31.fc35 local 2.0 M [1mcracklib [m i686 2.9.6-26.fc35 local 81 k [1mcracklib-dicts [m i686 2.9.6-26.fc35 local 3.6 M [1mcrypto-policies [m noarch 20210621-2.gita0e819e.fc35 local 58 k [1mcurl [m i686 7.78.0-3.fc35 local 303 k [1mcyrus-sasl-lib [m i686 2.1.27-12.fc35 local 850 k [1mdebugedit [m i686 5.0-2.fc35 local 77 k [1mdwz [m i686 0.14-2.fc35 local 132 k [1med [m i686 1.14.2-11.fc35 local 73 k [1mefi-srpm-macros [m noarch 5-3.fc35 local 22 k [1melfutils [m i686 0.185-5.fc35 local 531 k [1melfutils-debuginfod-client [m i686 0.185-5.fc35 local 37 k [1melfutils-default-yama-scope [m noarch 0.185-5.fc35 local 18 k [1melfutils-libelf [m i686 0.185-5.fc35 local 200 k [1melfutils-libs [m i686 0.185-5.fc35 local 297 k [1mfedora-gpg-keys [m noarch 35-0.4 local 111 k [1mfedora-release-common [m noarch 35-0.14 local 21 k [1mfedora-release-identity-basic[m noarch 35-0.14 local 12 k [1mfedora-repos [m noarch 35-0.4 local 11 k [1mfedora-repos-rawhide [m noarch 35-0.4 local 10 k [1mfile [m i686 5.40-9.fc35 local 50 k [1mfile-libs [m i686 5.40-9.fc35 local 627 k [1mfilesystem [m i686 3.14-7.fc35 local 1.1 M [1mfonts-srpm-macros [m noarch 1:2.0.5-6.fc35 local 27 k [1mfpc-srpm-macros [m noarch 1.3-4.fc35 local 7.6 k [1mgdb-minimal [m i686 10.2-6.fc35 local 3.8 M [1mgdbm-libs [m i686 1:1.20-2.fc35 local 59 k [1mghc-srpm-macros [m noarch 1.5.0-5.fc35 local 7.8 k [1mglibc [m i686 2.34-1.fc35 local 2.0 M [1mglibc-common [m i686 2.34-1.fc35 local 1.7 M [1mglibc-gconv-extra [m i686 2.34-1.fc35 local 1.7 M [1mgmp [m i686 1:6.2.0-7.fc35 local 303 k [1mgnat-srpm-macros [m noarch 4-14.fc35 local 8.2 k [1mgo-srpm-macros [m noarch 3.0.11-2.fc35 local 25 k [1mkernel-srpm-macros [m noarch 1.0-6.fc35 local 8.0 k [1mkeyutils-libs [m i686 1.6.1-3.fc35 local 31 k [1mkrb5-libs [m i686 1.19.2-1.fc35 local 773 k [1mlibacl [m i686 2.3.1-2.fc35 local 25 k [1mlibarchive [m i686 3.5.1-3.fc35 local 433 k [1mlibattr [m i686 2.5.1-3.fc35 local 18 k [1mlibblkid [m i686 2.37-6.fc35 local 118 k [1mlibbrotli [m i686 1.0.9-6.fc35 local 315 k [1mlibcap [m i686 2.48-3.fc35 local 68 k [1mlibcap-ng [m i686 0.8.2-6.fc35 local 33 k [1mlibcom_err [m i686 1.46.3-1.fc35 local 26 k [1mlibcurl [m i686 7.78.0-3.fc35 local 316 k [1mlibdb [m i686 5.3.28-47.fc35 local 817 k [1mlibeconf [m i686 0.4.0-2.fc35 local 29 k [1mlibfdisk [m i686 2.37-6.fc35 local 170 k [1mlibffi [m i686 3.1-28.fc34 local 32 k [1mlibgcc [m i686 11.2.1-1.fc35 local 116 k [1mlibgcrypt [m i686 1.9.3-4.fc35 local 474 k [1mlibgomp [m i686 11.2.1-1.fc35 local 287 k [1mlibgpg-error [m i686 1.42-3.fc35 local 216 k [1mlibidn2 [m i686 2.3.2-2.fc35 local 104 k [1mlibmount [m i686 2.37-6.fc35 local 142 k [1mlibnghttp2 [m i686 1.44.0-2.fc35 local 75 k [1mlibnsl2 [m i686 1.3.0-4.fc35 local 60 k [1mlibpkgconf [m i686 1.8.0-1.fc35 local 39 k [1mlibpsl [m i686 0.21.1-4.fc35 local 64 k [1mlibpwquality [m i686 1.4.4-5.fc35 local 105 k [1mlibselinux [m i686 3.2-4.fc35 local 89 k [1mlibsemanage [m i686 3.2-4.fc35 local 124 k [1mlibsepol [m i686 3.2-3.fc35 local 316 k [1mlibsigsegv [m i686 2.13-3.fc35 local 27 k [1mlibsmartcols [m i686 2.37-6.fc35 local 66 k [1mlibssh [m i686 0.9.5-3.fc35 local 220 k [1mlibssh-config [m noarch 0.9.5-3.fc35 local 9.1 k [1mlibstdc++ [m i686 11.2.1-1.fc35 local 790 k [1mlibtasn1 [m i686 4.16.0-6.fc35 local 75 k [1mlibtirpc [m i686 1.3.2-1.fc35 local 101 k [1mlibunistring [m i686 0.9.10-14.fc35 local 498 k [1mlibutempter [m i686 1.2.1-5.fc35 local 26 k [1mlibuuid [m i686 2.37-6.fc35 local 29 k [1mlibverto [m i686 0.3.2-2.fc35 local 21 k [1mlibxcrypt [m i686 4.4.24-1.fc35 local 123 k [1mlibxml2 [m i686 2.9.12-6.fc35 local 778 k [1mlibzstd [m i686 1.5.0-2.fc35 local 357 k [1mlua-libs [m i686 5.4.3-2.fc35 local 237 k [1mlua-srpm-macros [m noarch 1-5.fc35 local 8.4 k [1mlz4-libs [m i686 1.9.3-3.fc35 local 69 k [1mmpfr [m i686 4.1.0-8.fc35 local 355 k [1mncurses-base [m noarch 6.2-8.20210508.fc35 local 61 k [1mncurses-libs [m i686 6.2-8.20210508.fc35 local 345 k [1mnim-srpm-macros [m noarch 3-5.fc35 local 8.4 k [1mocaml-srpm-macros [m noarch 6-5.fc35 local 7.8 k [1mopenblas-srpm-macros [m noarch 2-10.fc35 local 7.4 k [1mopenldap [m i686 2.4.59-2.fc35 local 275 k [1mopenssl-libs [m i686 1:1.1.1k-2.fc35 local 1.4 M [1mp11-kit [m i686 0.23.22-4.fc35 local 334 k [1mp11-kit-trust [m i686 0.23.22-4.fc35 local 134 k [1mpam [m i686 1.5.1-9.fc35 local 562 k [1mpcre [m i686 8.44-3.fc35.2 local 194 k [1mpcre2 [m i686 10.37-4.fc35 local 227 k [1mpcre2-syntax [m noarch 10.37-4.fc35 local 142 k [1mperl-srpm-macros [m noarch 1-42.fc35 local 8.3 k [1mpkgconf [m i686 1.8.0-1.fc35 local 42 k [1mpkgconf-m4 [m noarch 1.8.0-1.fc35 local 14 k [1mpkgconf-pkg-config [m i686 1.8.0-1.fc35 local 10 k [1mpopt [m i686 1.18-6.fc35 local 61 k [1mpublicsuffix-list-dafsa [m noarch 20210518-2.fc35 local 58 k [1mpython-srpm-macros [m noarch 3.10-7.fc35 local 24 k [1mqt5-srpm-macros [m noarch 5.15.2-3.fc35 local 8.2 k [1mreadline [m i686 8.1-3.fc35 local 216 k [1mrpm [m i686 4.17.0-0.beta1.0.fc35.2 local 537 k [1mrpm-build-libs [m i686 4.17.0-0.beta1.0.fc35.2 local 102 k [1mrpm-libs [m i686 4.17.0-0.beta1.0.fc35.2 local 346 k [1mrpmautospec-rpm-macros [m noarch 0.2.5-1.fc35 local 9.9 k [1mrust-srpm-macros [m noarch 18-2.fc35 local 9.4 k [1msetup [m noarch 2.13.9.1-2.fc35 local 143 k [1msqlite-libs [m i686 3.36.0-3.fc35 local 679 k [1msystemd-libs [m i686 249.2-1.fc35 local 645 k [1mtzdata [m noarch 2021a-2.fc35 local 429 k [1mutil-linux-core [m i686 2.37-6.fc35 local 447 k [1mxxhash-libs [m i686 0.8.0-4.fc35 local 53 k [1mxz-libs [m i686 5.2.5-7.fc35 local 100 k [1mzip [m i686 3.0-31.fc35 local 261 k [1mzlib [m i686 1.2.11-30.fc35 local 93 k [1mzstd [m i686 1.5.0-2.fc35 local 620 k Installing Groups: build Transaction Summary ================================================================================ Install 148 Packages Total download size: 56 M Installed size: 190 M Downloading Packages: (1/148): basesystem-11-12.fc35.noarch.rpm 78 kB/s | 7.0 kB 00:00 (2/148): alternatives-1.19-1.fc35.i686.rpm 338 kB/s | 36 kB 00:00 (3/148): audit-libs-3.0.4-1.fc35.i686.rpm 1.1 MB/s | 121 kB 00:00 (4/148): binutils-gold-2.37-3.fc35.i686.rpm 23 MB/s | 806 kB 00:00 (5/148): bzip2-1.0.8-9.fc35.i686.rpm 4.1 MB/s | 52 kB 00:00 (6/148): bash-5.1.8-2.fc35.i686.rpm 23 MB/s | 1.7 MB 00:00 (7/148): bzip2-libs-1.0.8-9.fc35.i686.rpm 2.7 MB/s | 40 kB 00:00 (8/148): ca-certificates-2021.2.50-3.fc35.noarc 20 MB/s | 352 kB 00:00 (9/148): coreutils-8.32-31.fc35.i686.rpm 20 MB/s | 1.2 MB 00:00 (10/148): coreutils-common-8.32-31.fc35.i686.rp 31 MB/s | 2.0 MB 00:00 (11/148): cracklib-2.9.6-26.fc35.i686.rpm 5.6 MB/s | 81 kB 00:00 (12/148): cpio-2.13-11.fc35.i686.rpm 9.3 MB/s | 274 kB 00:00 (13/148): binutils-2.37-3.fc35.i686.rpm 37 MB/s | 6.0 MB 00:00 (14/148): crypto-policies-20210621-2.gita0e819e 4.8 MB/s | 58 kB 00:00 (15/148): curl-7.78.0-3.fc35.i686.rpm 17 MB/s | 303 kB 00:00 (16/148): cyrus-sasl-lib-2.1.27-12.fc35.i686.rp 34 MB/s | 850 kB 00:00 (17/148): debugedit-5.0-2.fc35.i686.rpm 5.4 MB/s | 77 kB 00:00 (18/148): diffutils-3.8-1.fc35.i686.rpm 25 MB/s | 410 kB 00:00 (19/148): dwz-0.14-2.fc35.i686.rpm 8.1 MB/s | 132 kB 00:00 (20/148): ed-1.14.2-11.fc35.i686.rpm 6.4 MB/s | 73 kB 00:00 (21/148): efi-srpm-macros-5-3.fc35.noarch.rpm 1.8 MB/s | 22 kB 00:00 (22/148): elfutils-debuginfod-client-0.185-5.fc 2.6 MB/s | 37 kB 00:00 (23/148): elfutils-0.185-5.fc35.i686.rpm 28 MB/s | 531 kB 00:00 (24/148): cracklib-dicts-2.9.6-26.fc35.i686.rpm 40 MB/s | 3.6 MB 00:00 (25/148): elfutils-default-yama-scope-0.185-5.f 1.5 MB/s | 18 kB 00:00 (26/148): elfutils-libelf-0.185-5.fc35.i686.rpm 16 MB/s | 200 kB 00:00 (27/148): elfutils-libs-0.185-5.fc35.i686.rpm 22 MB/s | 297 kB 00:00 (28/148): fedora-release-35-0.14.noarch.rpm 1.1 MB/s | 11 kB 00:00 (29/148): fedora-gpg-keys-35-0.4.noarch.rpm 7.6 MB/s | 111 kB 00:00 (30/148): fedora-release-common-35-0.14.noarch. 1.6 MB/s | 21 kB 00:00 (31/148): fedora-release-identity-basic-35-0.14 1.1 MB/s | 12 kB 00:00 (32/148): fedora-repos-35-0.4.noarch.rpm 969 kB/s | 11 kB 00:00 (33/148): fedora-repos-rawhide-35-0.4.noarch.rp 991 kB/s | 10 kB 00:00 (34/148): file-5.40-9.fc35.i686.rpm 2.2 MB/s | 50 kB 00:00 (35/148): file-libs-5.40-9.fc35.i686.rpm 24 MB/s | 627 kB 00:00 (36/148): filesystem-3.14-7.fc35.i686.rpm 39 MB/s | 1.1 MB 00:00 (37/148): fonts-srpm-macros-2.0.5-6.fc35.noarch 2.1 MB/s | 27 kB 00:00 (38/148): findutils-4.8.0-4.fc35.i686.rpm 25 MB/s | 548 kB 00:00 (39/148): fpc-srpm-macros-1.3-4.fc35.noarch.rpm 821 kB/s | 7.6 kB 00:00 (40/148): gdbm-libs-1.20-2.fc35.i686.rpm 4.9 MB/s | 59 kB 00:00 (41/148): gawk-5.1.0-4.fc35.i686.rpm 33 MB/s | 988 kB 00:00 (42/148): ghc-srpm-macros-1.5.0-5.fc35.noarch.r 749 kB/s | 7.8 kB 00:00 (43/148): glibc-2.34-1.fc35.i686.rpm 33 MB/s | 2.0 MB 00:00 (44/148): glibc-common-2.34-1.fc35.i686.rpm 27 MB/s | 1.7 MB 00:00 (45/148): glibc-minimal-langpack-2.34-1.fc35.i6 9.9 MB/s | 141 kB 00:00 (46/148): gdb-minimal-10.2-6.fc35.i686.rpm 31 MB/s | 3.8 MB 00:00 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libcap-ng-0.8.2-6.fc35.i686.rpm 2.6 MB/s | 33 kB 00:00 (63/148): libcom_err-1.46.3-1.fc35.i686.rpm 2.2 MB/s | 26 kB 00:00 (64/148): libcap-2.48-3.fc35.i686.rpm 3.7 MB/s | 68 kB 00:00 (65/148): libcurl-7.78.0-3.fc35.i686.rpm 16 MB/s | 316 kB 00:00 (66/148): libeconf-0.4.0-2.fc35.i686.rpm 1.5 MB/s | 29 kB 00:00 (67/148): libdb-5.3.28-47.fc35.i686.rpm 28 MB/s | 817 kB 00:00 (68/148): libfdisk-2.37-6.fc35.i686.rpm 13 MB/s | 170 kB 00:00 (69/148): libffi-3.1-28.fc34.i686.rpm 2.5 MB/s | 32 kB 00:00 (70/148): libgcc-11.2.1-1.fc35.i686.rpm 8.3 MB/s | 116 kB 00:00 (71/148): libgomp-11.2.1-1.fc35.i686.rpm 15 MB/s | 287 kB 00:00 (72/148): libgcrypt-1.9.3-4.fc35.i686.rpm 20 MB/s | 474 kB 00:00 (73/148): libgpg-error-1.42-3.fc35.i686.rpm 15 MB/s | 216 kB 00:00 (74/148): libidn2-2.3.2-2.fc35.i686.rpm 7.4 MB/s | 104 kB 00:00 (75/148): libmount-2.37-6.fc35.i686.rpm 11 MB/s | 142 kB 00:00 (76/148): libnghttp2-1.44.0-2.fc35.i686.rpm 5.9 MB/s | 75 kB 00:00 (77/148): libnsl2-1.3.0-4.fc35.i686.rpm 4.3 MB/s 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Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.14-7.fc35.i686 1/1 Preparing : 1/1 Installing : crypto-policies-20210621-2.gita0e819e.fc35.noarc 1/148 Running scriptlet: crypto-policies-20210621-2.gita0e819e.fc35.noarc 1/148 Installing : fedora-release-identity-basic-35-0.14.noarch 2/148 Installing : tzdata-2021a-2.fc35.noarch 3/148 Installing : rust-srpm-macros-18-2.fc35.noarch 4/148 Installing : qt5-srpm-macros-5.15.2-3.fc35.noarch 5/148 Installing : publicsuffix-list-dafsa-20210518-2.fc35.noarch 6/148 Installing : pkgconf-m4-1.8.0-1.fc35.noarch 7/148 Installing : perl-srpm-macros-1-42.fc35.noarch 8/148 Installing : pcre2-syntax-10.37-4.fc35.noarch 9/148 Installing : openblas-srpm-macros-2-10.fc35.noarch 10/148 Installing : ocaml-srpm-macros-6-5.fc35.noarch 11/148 Installing : nim-srpm-macros-3-5.fc35.noarch 12/148 Installing : ncurses-base-6.2-8.20210508.fc35.noarch 13/148 Installing : libssh-config-0.9.5-3.fc35.noarch 14/148 Installing : kernel-srpm-macros-1.0-6.fc35.noarch 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elfutils-libs-0.185-5.fc35.i686 121/148 Installing : elfutils-debuginfod-client-0.185-5.fc35.i686 122/148 Installing : binutils-gold-2.37-3.fc35.i686 123/148 Installing : binutils-2.37-3.fc35.i686 124/148 Running scriptlet: binutils-2.37-3.fc35.i686 124/148 Installing : elfutils-0.185-5.fc35.i686 125/148 Installing : curl-7.78.0-3.fc35.i686 126/148 Installing : libarchive-3.5.1-3.fc35.i686 127/148 Installing : rpm-4.17.0-0.beta1.0.fc35.2.i686 128/148 Installing : rpm-libs-4.17.0-0.beta1.0.fc35.2.i686 129/148 Installing : efi-srpm-macros-5-3.fc35.noarch 130/148 Installing : lua-srpm-macros-1-5.fc35.noarch 131/148 Installing : rpmautospec-rpm-macros-0.2.5-1.fc35.noarch 132/148 Installing : fonts-srpm-macros-1:2.0.5-6.fc35.noarch 133/148 Installing : go-srpm-macros-3.0.11-2.fc35.noarch 134/148 Installing : python-srpm-macros-3.10-7.fc35.noarch 135/148 Installing : redhat-rpm-config-194-1.fc35.noarch 136/148 Installing : rpm-build-libs-4.17.0-0.beta1.0.fc35.2.i686 137/148 Installing : libsemanage-3.2-4.fc35.i686 138/148 Installing : shadow-utils-2:4.9-1.fc35.i686 139/148 Running scriptlet: libutempter-1.2.1-5.fc35.i686 140/148 Installing : libutempter-1.2.1-5.fc35.i686 140/148 Installing : patch-2.7.6-15.fc35.i686 141/148 Installing : tar-2:1.34-2.fc35.i686 142/148 Installing : xxhash-libs-0.8.0-4.fc35.i686 143/148 Installing : gdb-minimal-10.2-6.fc35.i686 144/148 Installing : debugedit-5.0-2.fc35.i686 145/148 Installing : rpm-build-4.17.0-0.beta1.0.fc35.2.i686 146/148 Installing : util-linux-2.37-6.fc35.i686 147/148 Running scriptlet: util-linux-2.37-6.fc35.i686 147/148 Installing : which-2.21-27.fc35.i686 148/148 Running scriptlet: filesystem-3.14-7.fc35.i686 148/148 Running scriptlet: ca-certificates-2021.2.50-3.fc35.noarch 148/148 Running scriptlet: pam-1.5.1-9.fc35.i686 148/148 Running scriptlet: rpm-4.17.0-0.beta1.0.fc35.2.i686 148/148 Running scriptlet: which-2.21-27.fc35.i686 148/148 Verifying : alternatives-1.19-1.fc35.i686 1/148 Verifying : audit-libs-3.0.4-1.fc35.i686 2/148 Verifying : basesystem-11-12.fc35.noarch 3/148 Verifying : bash-5.1.8-2.fc35.i686 4/148 Verifying : binutils-2.37-3.fc35.i686 5/148 Verifying : binutils-gold-2.37-3.fc35.i686 6/148 Verifying : bzip2-1.0.8-9.fc35.i686 7/148 Verifying : bzip2-libs-1.0.8-9.fc35.i686 8/148 Verifying : ca-certificates-2021.2.50-3.fc35.noarch 9/148 Verifying : coreutils-8.32-31.fc35.i686 10/148 Verifying : coreutils-common-8.32-31.fc35.i686 11/148 Verifying : cpio-2.13-11.fc35.i686 12/148 Verifying : cracklib-2.9.6-26.fc35.i686 13/148 Verifying : cracklib-dicts-2.9.6-26.fc35.i686 14/148 Verifying : crypto-policies-20210621-2.gita0e819e.fc35.noarc 15/148 Verifying : curl-7.78.0-3.fc35.i686 16/148 Verifying : cyrus-sasl-lib-2.1.27-12.fc35.i686 17/148 Verifying : debugedit-5.0-2.fc35.i686 18/148 Verifying : diffutils-3.8-1.fc35.i686 19/148 Verifying : dwz-0.14-2.fc35.i686 20/148 Verifying : ed-1.14.2-11.fc35.i686 21/148 Verifying : efi-srpm-macros-5-3.fc35.noarch 22/148 Verifying : elfutils-0.185-5.fc35.i686 23/148 Verifying : elfutils-debuginfod-client-0.185-5.fc35.i686 24/148 Verifying : elfutils-default-yama-scope-0.185-5.fc35.noarch 25/148 Verifying : elfutils-libelf-0.185-5.fc35.i686 26/148 Verifying : elfutils-libs-0.185-5.fc35.i686 27/148 Verifying : fedora-gpg-keys-35-0.4.noarch 28/148 Verifying : fedora-release-35-0.14.noarch 29/148 Verifying : fedora-release-common-35-0.14.noarch 30/148 Verifying : fedora-release-identity-basic-35-0.14.noarch 31/148 Verifying : fedora-repos-35-0.4.noarch 32/148 Verifying : fedora-repos-rawhide-35-0.4.noarch 33/148 Verifying : file-5.40-9.fc35.i686 34/148 Verifying : file-libs-5.40-9.fc35.i686 35/148 Verifying : filesystem-3.14-7.fc35.i686 36/148 Verifying : findutils-1:4.8.0-4.fc35.i686 37/148 Verifying : fonts-srpm-macros-1:2.0.5-6.fc35.noarch 38/148 Verifying : fpc-srpm-macros-1.3-4.fc35.noarch 39/148 Verifying : gawk-5.1.0-4.fc35.i686 40/148 Verifying : gdb-minimal-10.2-6.fc35.i686 41/148 Verifying : gdbm-libs-1:1.20-2.fc35.i686 42/148 Verifying : ghc-srpm-macros-1.5.0-5.fc35.noarch 43/148 Verifying : glibc-2.34-1.fc35.i686 44/148 Verifying : glibc-common-2.34-1.fc35.i686 45/148 Verifying : glibc-gconv-extra-2.34-1.fc35.i686 46/148 Verifying : glibc-minimal-langpack-2.34-1.fc35.i686 47/148 Verifying : gmp-1:6.2.0-7.fc35.i686 48/148 Verifying : gnat-srpm-macros-4-14.fc35.noarch 49/148 Verifying : go-srpm-macros-3.0.11-2.fc35.noarch 50/148 Verifying : grep-3.6-4.fc35.i686 51/148 Verifying : gzip-1.10-5.fc35.i686 52/148 Verifying : info-6.8-2.fc35.i686 53/148 Verifying : kernel-srpm-macros-1.0-6.fc35.noarch 54/148 Verifying : keyutils-libs-1.6.1-3.fc35.i686 55/148 Verifying : krb5-libs-1.19.2-1.fc35.i686 56/148 Verifying : libacl-2.3.1-2.fc35.i686 57/148 Verifying : libarchive-3.5.1-3.fc35.i686 58/148 Verifying : libattr-2.5.1-3.fc35.i686 59/148 Verifying : libblkid-2.37-6.fc35.i686 60/148 Verifying : libbrotli-1.0.9-6.fc35.i686 61/148 Verifying : libcap-2.48-3.fc35.i686 62/148 Verifying : libcap-ng-0.8.2-6.fc35.i686 63/148 Verifying : libcom_err-1.46.3-1.fc35.i686 64/148 Verifying : libcurl-7.78.0-3.fc35.i686 65/148 Verifying : libdb-5.3.28-47.fc35.i686 66/148 Verifying : libeconf-0.4.0-2.fc35.i686 67/148 Verifying : libfdisk-2.37-6.fc35.i686 68/148 Verifying : libffi-3.1-28.fc34.i686 69/148 Verifying : libgcc-11.2.1-1.fc35.i686 70/148 Verifying : libgcrypt-1.9.3-4.fc35.i686 71/148 Verifying : libgomp-11.2.1-1.fc35.i686 72/148 Verifying : libgpg-error-1.42-3.fc35.i686 73/148 Verifying : libidn2-2.3.2-2.fc35.i686 74/148 Verifying : libmount-2.37-6.fc35.i686 75/148 Verifying : libnghttp2-1.44.0-2.fc35.i686 76/148 Verifying : libnsl2-1.3.0-4.fc35.i686 77/148 Verifying : libpkgconf-1.8.0-1.fc35.i686 78/148 Verifying : libpsl-0.21.1-4.fc35.i686 79/148 Verifying : libpwquality-1.4.4-5.fc35.i686 80/148 Verifying : libselinux-3.2-4.fc35.i686 81/148 Verifying : libsemanage-3.2-4.fc35.i686 82/148 Verifying : libsepol-3.2-3.fc35.i686 83/148 Verifying : libsigsegv-2.13-3.fc35.i686 84/148 Verifying : libsmartcols-2.37-6.fc35.i686 85/148 Verifying : libssh-0.9.5-3.fc35.i686 86/148 Verifying : libssh-config-0.9.5-3.fc35.noarch 87/148 Verifying : libstdc++-11.2.1-1.fc35.i686 88/148 Verifying : libtasn1-4.16.0-6.fc35.i686 89/148 Verifying : libtirpc-1.3.2-1.fc35.i686 90/148 Verifying : libunistring-0.9.10-14.fc35.i686 91/148 Verifying : libutempter-1.2.1-5.fc35.i686 92/148 Verifying : libuuid-2.37-6.fc35.i686 93/148 Verifying : libverto-0.3.2-2.fc35.i686 94/148 Verifying : libxcrypt-4.4.24-1.fc35.i686 95/148 Verifying : libxml2-2.9.12-6.fc35.i686 96/148 Verifying : libzstd-1.5.0-2.fc35.i686 97/148 Verifying : lua-libs-5.4.3-2.fc35.i686 98/148 Verifying : lua-srpm-macros-1-5.fc35.noarch 99/148 Verifying : lz4-libs-1.9.3-3.fc35.i686 100/148 Verifying : mpfr-4.1.0-8.fc35.i686 101/148 Verifying : ncurses-base-6.2-8.20210508.fc35.noarch 102/148 Verifying : ncurses-libs-6.2-8.20210508.fc35.i686 103/148 Verifying : nim-srpm-macros-3-5.fc35.noarch 104/148 Verifying : ocaml-srpm-macros-6-5.fc35.noarch 105/148 Verifying : openblas-srpm-macros-2-10.fc35.noarch 106/148 Verifying : openldap-2.4.59-2.fc35.i686 107/148 Verifying : openssl-libs-1:1.1.1k-2.fc35.i686 108/148 Verifying : p11-kit-0.23.22-4.fc35.i686 109/148 Verifying : p11-kit-trust-0.23.22-4.fc35.i686 110/148 Verifying : pam-1.5.1-9.fc35.i686 111/148 Verifying : patch-2.7.6-15.fc35.i686 112/148 Verifying : pcre-8.44-3.fc35.2.i686 113/148 Verifying : pcre2-10.37-4.fc35.i686 114/148 Verifying : pcre2-syntax-10.37-4.fc35.noarch 115/148 Verifying : perl-srpm-macros-1-42.fc35.noarch 116/148 Verifying : pkgconf-1.8.0-1.fc35.i686 117/148 Verifying : pkgconf-m4-1.8.0-1.fc35.noarch 118/148 Verifying : pkgconf-pkg-config-1.8.0-1.fc35.i686 119/148 Verifying : popt-1.18-6.fc35.i686 120/148 Verifying : publicsuffix-list-dafsa-20210518-2.fc35.noarch 121/148 Verifying : python-srpm-macros-3.10-7.fc35.noarch 122/148 Verifying : qt5-srpm-macros-5.15.2-3.fc35.noarch 123/148 Verifying : readline-8.1-3.fc35.i686 124/148 Verifying : redhat-rpm-config-194-1.fc35.noarch 125/148 Verifying : rpm-4.17.0-0.beta1.0.fc35.2.i686 126/148 Verifying : rpm-build-4.17.0-0.beta1.0.fc35.2.i686 127/148 Verifying : rpm-build-libs-4.17.0-0.beta1.0.fc35.2.i686 128/148 Verifying : rpm-libs-4.17.0-0.beta1.0.fc35.2.i686 129/148 Verifying : rpmautospec-rpm-macros-0.2.5-1.fc35.noarch 130/148 Verifying : rust-srpm-macros-18-2.fc35.noarch 131/148 Verifying : sed-4.8-8.fc35.i686 132/148 Verifying : setup-2.13.9.1-2.fc35.noarch 133/148 Verifying : shadow-utils-2:4.9-1.fc35.i686 134/148 Verifying : sqlite-libs-3.36.0-3.fc35.i686 135/148 Verifying : systemd-libs-249.2-1.fc35.i686 136/148 Verifying : tar-2:1.34-2.fc35.i686 137/148 Verifying : tzdata-2021a-2.fc35.noarch 138/148 Verifying : unzip-6.0-53.fc35.i686 139/148 Verifying : util-linux-2.37-6.fc35.i686 140/148 Verifying : util-linux-core-2.37-6.fc35.i686 141/148 Verifying : which-2.21-27.fc35.i686 142/148 Verifying : xxhash-libs-0.8.0-4.fc35.i686 143/148 Verifying : xz-5.2.5-7.fc35.i686 144/148 Verifying : xz-libs-5.2.5-7.fc35.i686 145/148 Verifying : zip-3.0-31.fc35.i686 146/148 Verifying : zlib-1.2.11-30.fc35.i686 147/148 Verifying : zstd-1.5.0-2.fc35.i686 148/148 Installed: alternatives-1.19-1.fc35.i686 audit-libs-3.0.4-1.fc35.i686 basesystem-11-12.fc35.noarch bash-5.1.8-2.fc35.i686 binutils-2.37-3.fc35.i686 binutils-gold-2.37-3.fc35.i686 bzip2-1.0.8-9.fc35.i686 bzip2-libs-1.0.8-9.fc35.i686 ca-certificates-2021.2.50-3.fc35.noarch coreutils-8.32-31.fc35.i686 coreutils-common-8.32-31.fc35.i686 cpio-2.13-11.fc35.i686 cracklib-2.9.6-26.fc35.i686 cracklib-dicts-2.9.6-26.fc35.i686 crypto-policies-20210621-2.gita0e819e.fc35.noarch curl-7.78.0-3.fc35.i686 cyrus-sasl-lib-2.1.27-12.fc35.i686 debugedit-5.0-2.fc35.i686 diffutils-3.8-1.fc35.i686 dwz-0.14-2.fc35.i686 ed-1.14.2-11.fc35.i686 efi-srpm-macros-5-3.fc35.noarch elfutils-0.185-5.fc35.i686 elfutils-debuginfod-client-0.185-5.fc35.i686 elfutils-default-yama-scope-0.185-5.fc35.noarch elfutils-libelf-0.185-5.fc35.i686 elfutils-libs-0.185-5.fc35.i686 fedora-gpg-keys-35-0.4.noarch fedora-release-35-0.14.noarch fedora-release-common-35-0.14.noarch fedora-release-identity-basic-35-0.14.noarch fedora-repos-35-0.4.noarch fedora-repos-rawhide-35-0.4.noarch file-5.40-9.fc35.i686 file-libs-5.40-9.fc35.i686 filesystem-3.14-7.fc35.i686 findutils-1:4.8.0-4.fc35.i686 fonts-srpm-macros-1:2.0.5-6.fc35.noarch fpc-srpm-macros-1.3-4.fc35.noarch gawk-5.1.0-4.fc35.i686 gdb-minimal-10.2-6.fc35.i686 gdbm-libs-1:1.20-2.fc35.i686 ghc-srpm-macros-1.5.0-5.fc35.noarch glibc-2.34-1.fc35.i686 glibc-common-2.34-1.fc35.i686 glibc-gconv-extra-2.34-1.fc35.i686 glibc-minimal-langpack-2.34-1.fc35.i686 gmp-1:6.2.0-7.fc35.i686 gnat-srpm-macros-4-14.fc35.noarch go-srpm-macros-3.0.11-2.fc35.noarch grep-3.6-4.fc35.i686 gzip-1.10-5.fc35.i686 info-6.8-2.fc35.i686 kernel-srpm-macros-1.0-6.fc35.noarch keyutils-libs-1.6.1-3.fc35.i686 krb5-libs-1.19.2-1.fc35.i686 libacl-2.3.1-2.fc35.i686 libarchive-3.5.1-3.fc35.i686 libattr-2.5.1-3.fc35.i686 libblkid-2.37-6.fc35.i686 libbrotli-1.0.9-6.fc35.i686 libcap-2.48-3.fc35.i686 libcap-ng-0.8.2-6.fc35.i686 libcom_err-1.46.3-1.fc35.i686 libcurl-7.78.0-3.fc35.i686 libdb-5.3.28-47.fc35.i686 libeconf-0.4.0-2.fc35.i686 libfdisk-2.37-6.fc35.i686 libffi-3.1-28.fc34.i686 libgcc-11.2.1-1.fc35.i686 libgcrypt-1.9.3-4.fc35.i686 libgomp-11.2.1-1.fc35.i686 libgpg-error-1.42-3.fc35.i686 libidn2-2.3.2-2.fc35.i686 libmount-2.37-6.fc35.i686 libnghttp2-1.44.0-2.fc35.i686 libnsl2-1.3.0-4.fc35.i686 libpkgconf-1.8.0-1.fc35.i686 libpsl-0.21.1-4.fc35.i686 libpwquality-1.4.4-5.fc35.i686 libselinux-3.2-4.fc35.i686 libsemanage-3.2-4.fc35.i686 libsepol-3.2-3.fc35.i686 libsigsegv-2.13-3.fc35.i686 libsmartcols-2.37-6.fc35.i686 libssh-0.9.5-3.fc35.i686 libssh-config-0.9.5-3.fc35.noarch libstdc++-11.2.1-1.fc35.i686 libtasn1-4.16.0-6.fc35.i686 libtirpc-1.3.2-1.fc35.i686 libunistring-0.9.10-14.fc35.i686 libutempter-1.2.1-5.fc35.i686 libuuid-2.37-6.fc35.i686 libverto-0.3.2-2.fc35.i686 libxcrypt-4.4.24-1.fc35.i686 libxml2-2.9.12-6.fc35.i686 libzstd-1.5.0-2.fc35.i686 lua-libs-5.4.3-2.fc35.i686 lua-srpm-macros-1-5.fc35.noarch lz4-libs-1.9.3-3.fc35.i686 mpfr-4.1.0-8.fc35.i686 ncurses-base-6.2-8.20210508.fc35.noarch ncurses-libs-6.2-8.20210508.fc35.i686 nim-srpm-macros-3-5.fc35.noarch ocaml-srpm-macros-6-5.fc35.noarch openblas-srpm-macros-2-10.fc35.noarch openldap-2.4.59-2.fc35.i686 openssl-libs-1:1.1.1k-2.fc35.i686 p11-kit-0.23.22-4.fc35.i686 p11-kit-trust-0.23.22-4.fc35.i686 pam-1.5.1-9.fc35.i686 patch-2.7.6-15.fc35.i686 pcre-8.44-3.fc35.2.i686 pcre2-10.37-4.fc35.i686 pcre2-syntax-10.37-4.fc35.noarch perl-srpm-macros-1-42.fc35.noarch pkgconf-1.8.0-1.fc35.i686 pkgconf-m4-1.8.0-1.fc35.noarch pkgconf-pkg-config-1.8.0-1.fc35.i686 popt-1.18-6.fc35.i686 publicsuffix-list-dafsa-20210518-2.fc35.noarch python-srpm-macros-3.10-7.fc35.noarch qt5-srpm-macros-5.15.2-3.fc35.noarch readline-8.1-3.fc35.i686 redhat-rpm-config-194-1.fc35.noarch rpm-4.17.0-0.beta1.0.fc35.2.i686 rpm-build-4.17.0-0.beta1.0.fc35.2.i686 rpm-build-libs-4.17.0-0.beta1.0.fc35.2.i686 rpm-libs-4.17.0-0.beta1.0.fc35.2.i686 rpmautospec-rpm-macros-0.2.5-1.fc35.noarch rust-srpm-macros-18-2.fc35.noarch sed-4.8-8.fc35.i686 setup-2.13.9.1-2.fc35.noarch shadow-utils-2:4.9-1.fc35.i686 sqlite-libs-3.36.0-3.fc35.i686 systemd-libs-249.2-1.fc35.i686 tar-2:1.34-2.fc35.i686 tzdata-2021a-2.fc35.noarch unzip-6.0-53.fc35.i686 util-linux-2.37-6.fc35.i686 util-linux-core-2.37-6.fc35.i686 which-2.21-27.fc35.i686 xxhash-libs-0.8.0-4.fc35.i686 xz-5.2.5-7.fc35.i686 xz-libs-5.2.5-7.fc35.i686 zip-3.0-31.fc35.i686 zlib-1.2.11-30.fc35.i686 zstd-1.5.0-2.fc35.i686 Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: p11-kit-trust-0.23.22-4.fc35.i686 libcap-2.48-3.fc35.i686 debugedit-5.0-2.fc35.i686 libgpg-error-1.42-3.fc35.i686 info-6.8-2.fc35.i686 crypto-policies-20210621-2.gita0e819e.fc35.noarch mpfr-4.1.0-8.fc35.i686 zstd-1.5.0-2.fc35.i686 libgomp-11.2.1-1.fc35.i686 util-linux-2.37-6.fc35.i686 libarchive-3.5.1-3.fc35.i686 libffi-3.1-28.fc34.i686 libssh-config-0.9.5-3.fc35.noarch p11-kit-0.23.22-4.fc35.i686 libxml2-2.9.12-6.fc35.i686 popt-1.18-6.fc35.i686 libstdc++-11.2.1-1.fc35.i686 coreutils-common-8.32-31.fc35.i686 systemd-libs-249.2-1.fc35.i686 file-libs-5.40-9.fc35.i686 pkgconf-pkg-config-1.8.0-1.fc35.i686 shadow-utils-4.9-1.fc35.i686 pkgconf-m4-1.8.0-1.fc35.noarch pkgconf-1.8.0-1.fc35.i686 libtasn1-4.16.0-6.fc35.i686 libnghttp2-1.44.0-2.fc35.i686 gzip-1.10-5.fc35.i686 perl-srpm-macros-1-42.fc35.noarch ocaml-srpm-macros-6-5.fc35.noarch pam-1.5.1-9.fc35.i686 rpm-libs-4.17.0-0.beta1.0.fc35.2.i686 bzip2-1.0.8-9.fc35.i686 sed-4.8-8.fc35.i686 go-srpm-macros-3.0.11-2.fc35.noarch ncurses-libs-6.2-8.20210508.fc35.i686 libunistring-0.9.10-14.fc35.i686 coreutils-8.32-31.fc35.i686 pcre2-syntax-10.37-4.fc35.noarch qt5-srpm-macros-5.15.2-3.fc35.noarch bash-5.1.8-2.fc35.i686 ca-certificates-2021.2.50-3.fc35.noarch tar-1.34-2.fc35.i686 ghc-srpm-macros-1.5.0-5.fc35.noarch libpsl-0.21.1-4.fc35.i686 rpm-4.17.0-0.beta1.0.fc35.2.i686 elfutils-default-yama-scope-0.185-5.fc35.noarch elfutils-debuginfod-client-0.185-5.fc35.i686 keyutils-libs-1.6.1-3.fc35.i686 fonts-srpm-macros-2.0.5-6.fc35.noarch sqlite-libs-3.36.0-3.fc35.i686 gdbm-libs-1.20-2.fc35.i686 elfutils-libs-0.185-5.fc35.i686 openssl-libs-1.1.1k-2.fc35.i686 publicsuffix-list-dafsa-20210518-2.fc35.noarch libgcrypt-1.9.3-4.fc35.i686 findutils-4.8.0-4.fc35.i686 libacl-2.3.1-2.fc35.i686 lua-libs-5.4.3-2.fc35.i686 alternatives-1.19-1.fc35.i686 openldap-2.4.59-2.fc35.i686 openblas-srpm-macros-2-10.fc35.noarch libblkid-2.37-6.fc35.i686 util-linux-core-2.37-6.fc35.i686 fedora-repos-35-0.4.noarch libselinux-3.2-4.fc35.i686 libsigsegv-2.13-3.fc35.i686 libmount-2.37-6.fc35.i686 which-2.21-27.fc35.i686 libfdisk-2.37-6.fc35.i686 bzip2-libs-1.0.8-9.fc35.i686 gmp-6.2.0-7.fc35.i686 lz4-libs-1.9.3-3.fc35.i686 libzstd-1.5.0-2.fc35.i686 fedora-release-identity-basic-35-0.14.noarch libcap-ng-0.8.2-6.fc35.i686 filesystem-3.14-7.fc35.i686 cpio-2.13-11.fc35.i686 basesystem-11-12.fc35.noarch diffutils-3.8-1.fc35.i686 libbrotli-1.0.9-6.fc35.i686 zip-3.0-31.fc35.i686 libgcc-11.2.1-1.fc35.i686 lua-srpm-macros-1-5.fc35.noarch fedora-release-common-35-0.14.noarch xz-libs-5.2.5-7.fc35.i686 rpm-build-4.17.0-0.beta1.0.fc35.2.i686 kernel-srpm-macros-1.0-6.fc35.noarch unzip-6.0-53.fc35.i686 libverto-0.3.2-2.fc35.i686 ed-1.14.2-11.fc35.i686 dwz-0.14-2.fc35.i686 fpc-srpm-macros-1.3-4.fc35.noarch audit-libs-3.0.4-1.fc35.i686 grep-3.6-4.fc35.i686 redhat-rpm-config-194-1.fc35.noarch glibc-2.34-1.fc35.i686 cracklib-2.9.6-26.fc35.i686 fedora-release-35-0.14.noarch libutempter-1.2.1-5.fc35.i686 setup-2.13.9.1-2.fc35.noarch glibc-gconv-extra-2.34-1.fc35.i686 pcre2-10.37-4.fc35.i686 binutils-2.37-3.fc35.i686 rpm-build-libs-4.17.0-0.beta1.0.fc35.2.i686 libcom_err-1.46.3-1.fc35.i686 ncurses-base-6.2-8.20210508.fc35.noarch libpwquality-1.4.4-5.fc35.i686 gnat-srpm-macros-4-14.fc35.noarch zlib-1.2.11-30.fc35.i686 cracklib-dicts-2.9.6-26.fc35.i686 libnsl2-1.3.0-4.fc35.i686 libssh-0.9.5-3.fc35.i686 tzdata-2021a-2.fc35.noarch binutils-gold-2.37-3.fc35.i686 libtirpc-1.3.2-1.fc35.i686 nim-srpm-macros-3-5.fc35.noarch libsmartcols-2.37-6.fc35.i686 curl-7.78.0-3.fc35.i686 python-srpm-macros-3.10-7.fc35.noarch libuuid-2.37-6.fc35.i686 libcurl-7.78.0-3.fc35.i686 rpmautospec-rpm-macros-0.2.5-1.fc35.noarch krb5-libs-1.19.2-1.fc35.i686 xz-5.2.5-7.fc35.i686 libsemanage-3.2-4.fc35.i686 fedora-gpg-keys-35-0.4.noarch fedora-repos-rawhide-35-0.4.noarch readline-8.1-3.fc35.i686 pcre-8.44-3.fc35.2.i686 libdb-5.3.28-47.fc35.i686 efi-srpm-macros-5-3.fc35.noarch libeconf-0.4.0-2.fc35.i686 glibc-common-2.34-1.fc35.i686 elfutils-libelf-0.185-5.fc35.i686 gawk-5.1.0-4.fc35.i686 xxhash-libs-0.8.0-4.fc35.i686 elfutils-0.185-5.fc35.i686 libattr-2.5.1-3.fc35.i686 file-5.40-9.fc35.i686 libpkgconf-1.8.0-1.fc35.i686 cyrus-sasl-lib-2.1.27-12.fc35.i686 rust-srpm-macros-18-2.fc35.noarch patch-2.7.6-15.fc35.i686 glibc-minimal-langpack-2.34-1.fc35.i686 libxcrypt-4.4.24-1.fc35.i686 libsepol-3.2-3.fc35.i686 libidn2-2.3.2-2.fc35.i686 gdb-minimal-10.2-6.fc35.i686 Start: buildsrpm Start: rpmbuild -bs Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1626998400 Wrote: /builddir/build/SRPMS/bcftools-1.13-1.fc35.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-i686-1628447957.888446/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-i686-1628447957.888446/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-i686-1628447957.888446/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-nytxz3sl/bcftools/bcftools.spec) Config(child) 0 minutes 31 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=18000): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/bcftools-1.13-1.fc35.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1628447957.888446 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 2.12 starting (python version = 3.9.4, NVR = mock-2.12-1.fc34)... 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-1.13-1.fc35.src.rpm) Config(fedora-rawhide-i686) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-1628447957.888446/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: 2.12 INFO: Mock Version: 2.12 Start: dnf update No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 72 kB/s | 3.3 kB 00:00 local 105 kB/s | 3.8 kB 00:00 Dependencies resolved. Nothing to do. Complete! Finish: dnf update Finish: chroot init Start: build phase for bcftools-1.13-1.fc35.src.rpm Start: build setup for bcftools-1.13-1.fc35.src.rpm Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1626998400 Wrote: /builddir/build/SRPMS/bcftools-1.13-1.fc35.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 74 kB/s | 3.3 kB 00:00 local 81 kB/s | 3.8 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: [1mgcc [m i686 11.2.1-1.fc35 local 31 M [1mgsl-devel [m i686 2.6-5.fc35 local 590 k [1mhtslib-devel [m i686 1.13-1.fc35 copr_base 98 k [1mhtslib-tools [m i686 1.13-1.fc35 copr_base 559 k [1mmake [m i686 1:4.3-6.fc35 local 540 k [1mperl-ExtUtils-Embed [m noarch 1.35-481.fc35 local 27 k [1mperl-File-Temp [m noarch 1:0.231.100-478.fc35 local 59 k [1mperl-FindBin [m noarch 1.52-481.fc35 local 23 k [1mperl-Getopt-Long [m noarch 1:2.52-478.fc35 local 60 k [1mperl-interpreter [m i686 4:5.34.0-481.fc35 local 80 k [1mzlib-devel [m i686 1.2.11-30.fc35 local 44 k Installing dependencies: [1mannobin-docs [m noarch 9.83-1.fc35 local 78 k [1mannobin-plugin-gcc [m i686 9.83-1.fc35 local 44 k [1mautoconf [m noarch 2.69-37.fc35 local 666 k [1mautomake [m noarch 1.16.2-5.fc35 local 662 k [1mcpp [m i686 11.2.1-1.fc35 local 9.9 M [1memacs-filesystem [m noarch 1:27.2-9.fc35 local 9.0 k [1mexpat [m i686 2.4.1-2.fc35 local 113 k [1mgc [m i686 8.0.4-6.fc35 local 105 k [1mglibc-devel [m i686 2.34-1.fc35 local 154 k [1mglibc-headers-x86 [m noarch 2.34-1.fc35 local 551 k [1mgroff-base [m i686 1.22.4-8.fc35 local 1.0 M [1mgsl [m i686 2.6-5.fc35 local 1.1 M [1mguile22 [m i686 2.2.7-3.fc35 local 6.5 M [1mhtslib [m i686 1.13-1.fc35 copr_base 508 k [1mkernel-headers [m i686 5.14.0-0.rc4.git0.1.fc35 local 1.3 M [1mlibasan [m i686 11.2.1-1.fc35 local 445 k [1mlibatomic [m i686 11.2.1-1.fc35 local 47 k [1mlibmpc [m i686 1.2.1-3.fc35 local 67 k [1mlibtool-ltdl [m i686 2.4.6-42.fc35 local 38 k [1mlibubsan [m i686 11.2.1-1.fc35 local 218 k [1mlibxcrypt-devel [m i686 4.4.24-1.fc35 local 29 k [1mm4 [m i686 1.4.19-2.fc35 local 299 k [1mmpdecimal [m i686 2.5.1-2.fc35 local 106 k [1mncurses [m i686 6.2-8.20210508.fc35 local 403 k [1mperl-AutoSplit [m noarch 5.74-481.fc35 local 31 k [1mperl-B [m i686 1.82-481.fc35 local 193 k [1mperl-Benchmark [m noarch 1.23-481.fc35 local 36 k [1mperl-Carp [m noarch 1.52-478.fc35 local 29 k [1mperl-Class-Struct [m noarch 0.66-481.fc35 local 31 k [1mperl-Data-Dumper [m i686 2.183-2.fc35 local 57 k [1mperl-Devel-PPPort [m i686 3.63-2.fc35 local 221 k [1mperl-DynaLoader [m i686 1.50-481.fc35 local 35 k [1mperl-Encode [m i686 4:3.11-479.fc35 local 1.2 M [1mperl-Errno [m i686 1.33-481.fc35 local 24 k [1mperl-Exporter [m noarch 5.76-479.fc35 local 31 k [1mperl-ExtUtils-Command [m noarch 2:7.62-479.fc35 local 15 k [1mperl-ExtUtils-Constant [m noarch 0.25-481.fc35 local 56 k [1mperl-ExtUtils-Install [m noarch 2.20-478.fc35 local 44 k [1mperl-ExtUtils-MakeMaker[m noarch 2:7.62-479.fc35 local 289 k [1mperl-ExtUtils-Manifest [m noarch 1:1.73-478.fc35 local 34 k [1mperl-ExtUtils-ParseXS [m noarch 1:3.43-478.fc35 local 182 k [1mperl-Fcntl [m i686 1.14-481.fc35 local 30 k [1mperl-File-Basename [m noarch 2.85-481.fc35 local 26 k [1mperl-File-Compare [m noarch 1.100.600-481.fc35 local 22 k [1mperl-File-Copy [m noarch 2.35-481.fc35 local 29 k [1mperl-File-Find [m noarch 1.39-481.fc35 local 35 k [1mperl-File-Path [m noarch 2.18-478.fc35 local 35 k [1mperl-File-stat [m noarch 1.09-481.fc35 local 26 k [1mperl-Getopt-Std [m noarch 1.13-481.fc35 local 25 k [1mperl-HTTP-Tiny [m noarch 0.078-1.fc35 local 55 k [1mperl-IO [m i686 1.46-481.fc35 local 97 k [1mperl-IPC-Open3 [m noarch 1.21-481.fc35 local 32 k [1mperl-MIME-Base64 [m i686 3.16-478.fc35 local 30 k [1mperl-POSIX [m i686 1.97-481.fc35 local 110 k [1mperl-PathTools [m i686 3.80-478.fc35 local 85 k [1mperl-Pod-Escapes [m noarch 1:1.07-478.fc35 local 20 k [1mperl-Pod-Perldoc [m noarch 3.28.01-479.fc35 local 84 k [1mperl-Pod-Simple [m noarch 1:3.43-2.fc35 local 215 k [1mperl-Pod-Usage [m noarch 4:2.01-478.fc35 local 40 k [1mperl-Scalar-List-Utils [m i686 5:1.56-461.fc35 local 74 k [1mperl-SelectSaver [m noarch 1.02-481.fc35 local 21 k [1mperl-Socket [m i686 4:2.032-2.fc35 local 56 k [1mperl-Storable [m i686 1:3.23-478.fc35 local 97 k [1mperl-Symbol [m noarch 1.09-481.fc35 local 23 k [1mperl-Term-ANSIColor [m noarch 5.01-479.fc35 local 48 k [1mperl-Term-Cap [m noarch 1.17-478.fc35 local 22 k [1mperl-Test-Harness [m noarch 1:3.43-479.fc35 local 267 k [1mperl-Text-ParseWords [m noarch 3.30-478.fc35 local 16 k [1mperl-Text-Tabs+Wrap [m noarch 2021.0726-1.fc35 local 22 k [1mperl-Thread-Queue [m noarch 3.14-478.fc35 local 21 k [1mperl-Time-Local [m noarch 2:1.300-478.fc35 local 33 k [1mperl-base [m noarch 2.27-481.fc35 local 25 k [1mperl-constant [m noarch 1.33-479.fc35 local 23 k [1mperl-devel [m i686 4:5.34.0-481.fc35 local 680 k [1mperl-if [m noarch 0.60.900-481.fc35 local 23 k [1mperl-lib [m i686 0.65-481.fc35 local 24 k [1mperl-libs [m i686 4:5.34.0-481.fc35 local 2.2 M [1mperl-locale [m noarch 1.10-481.fc35 local 23 k [1mperl-mro [m i686 1.25-481.fc35 local 38 k [1mperl-overload [m noarch 1.33-481.fc35 local 55 k [1mperl-overloading [m noarch 0.02-481.fc35 local 22 k [1mperl-parent [m noarch 1:0.238-478.fc35 local 14 k [1mperl-podlators [m noarch 1:4.14-478.fc35 local 111 k [1mperl-subs [m noarch 1.04-481.fc35 local 21 k [1mperl-threads [m i686 1:2.26-448.fc35 local 59 k [1mperl-threads-shared [m i686 1.62-478.fc35 local 44 k [1mperl-vars [m noarch 1.05-481.fc35 local 22 k [1mperl-version [m i686 8:0.99.29-4.fc35 local 63 k [1mpython-pip-wheel [m noarch 21.1.3-2.fc35 local 1.3 M [1mpython-setuptools-wheel[m noarch 57.4.0-1.fc35 local 505 k [1mpython3 [m i686 3.10.0~rc1-1.fc35 local 25 k [1mpython3-libs [m i686 3.10.0~rc1-1.fc35 local 7.5 M [1mpython3-pyparsing [m noarch 2.4.7-9.fc35 local 151 k [1msystemtap-sdt-devel [m i686 4.6~pre16262021g84ef6bd9-2.fc35 local 71 k Transaction Summary ================================================================================ Install 105 Packages Total download size: 74 M Installed size: 239 M Downloading Packages: (1/105): htslib-devel-1.13-1.fc35.i686.rpm 2.0 MB/s | 98 kB 00:00 (2/105): htslib-tools-1.13-1.fc35.i686.rpm 7.4 MB/s | 559 kB 00:00 (3/105): htslib-1.13-1.fc35.i686.rpm 6.1 MB/s | 508 kB 00:00 (4/105): annobin-docs-9.83-1.fc35.noarch.rpm 1.2 MB/s | 78 kB 00:00 (5/105): annobin-plugin-gcc-9.83-1.fc35.i686.rp 836 kB/s | 44 kB 00:00 (6/105): automake-1.16.2-5.fc35.noarch.rpm 13 MB/s | 662 kB 00:00 (7/105): emacs-filesystem-27.2-9.fc35.noarch.rp 608 kB/s | 9.0 kB 00:00 (8/105): autoconf-2.69-37.fc35.noarch.rpm 6.4 MB/s | 666 kB 00:00 (9/105): expat-2.4.1-2.fc35.i686.rpm 6.6 MB/s | 113 kB 00:00 (10/105): gc-8.0.4-6.fc35.i686.rpm 8.1 MB/s | 105 kB 00:00 (11/105): glibc-devel-2.34-1.fc35.i686.rpm 9.7 MB/s | 154 kB 00:00 (12/105): glibc-headers-x86-2.34-1.fc35.noarch. 13 MB/s | 551 kB 00:00 (13/105): groff-base-1.22.4-8.fc35.i686.rpm 21 MB/s | 1.0 MB 00:00 (14/105): cpp-11.2.1-1.fc35.i686.rpm 30 MB/s | 9.9 MB 00:00 (15/105): gsl-devel-2.6-5.fc35.i686.rpm 17 MB/s | 590 kB 00:00 (16/105): gsl-2.6-5.fc35.i686.rpm 4.0 MB/s | 1.1 MB 00:00 (17/105): kernel-headers-5.14.0-0.rc4.git0.1.fc 29 MB/s | 1.3 MB 00:00 (18/105): libasan-11.2.1-1.fc35.i686.rpm 18 MB/s | 445 kB 00:00 (19/105): libatomic-11.2.1-1.fc35.i686.rpm 3.7 MB/s | 47 kB 00:00 (20/105): libmpc-1.2.1-3.fc35.i686.rpm 4.9 MB/s | 67 kB 00:00 (21/105): libtool-ltdl-2.4.6-42.fc35.i686.rpm 3.0 MB/s | 38 kB 00:00 (22/105): libubsan-11.2.1-1.fc35.i686.rpm 12 MB/s | 218 kB 00:00 (23/105): libxcrypt-devel-4.4.24-1.fc35.i686.rp 2.3 MB/s | 29 kB 00:00 (24/105): m4-1.4.19-2.fc35.i686.rpm 15 MB/s | 299 kB 00:00 (25/105): guile22-2.2.7-3.fc35.i686.rpm 25 MB/s | 6.5 MB 00:00 (26/105): mpdecimal-2.5.1-2.fc35.i686.rpm 7.2 MB/s | 106 kB 00:00 (27/105): make-4.3-6.fc35.i686.rpm 20 MB/s | 540 kB 00:00 (28/105): perl-AutoSplit-5.74-481.fc35.noarch.r 2.2 MB/s | 31 kB 00:00 (29/105): ncurses-6.2-8.20210508.fc35.i686.rpm 18 MB/s | 403 kB 00:00 (30/105): perl-B-1.82-481.fc35.i686.rpm 11 MB/s | 193 kB 00:00 (31/105): perl-Benchmark-1.23-481.fc35.noarch.r 3.1 MB/s | 36 kB 00:00 (32/105): perl-Class-Struct-0.66-481.fc35.noarc 2.8 MB/s | 31 kB 00:00 (33/105): perl-Carp-1.52-478.fc35.noarch.rpm 2.3 MB/s | 29 kB 00:00 (34/105): gcc-11.2.1-1.fc35.i686.rpm 47 MB/s | 31 MB 00:00 (35/105): perl-Data-Dumper-2.183-2.fc35.i686.rp 1.4 MB/s | 57 kB 00:00 (36/105): perl-Devel-PPPort-3.63-2.fc35.i686.rp 5.2 MB/s | 221 kB 00:00 (37/105): perl-DynaLoader-1.50-481.fc35.i686.rp 2.7 MB/s | 35 kB 00:00 (38/105): perl-Errno-1.33-481.fc35.i686.rpm 2.0 MB/s | 24 kB 00:00 (39/105): perl-Exporter-5.76-479.fc35.noarch.rp 2.4 MB/s | 31 kB 00:00 (40/105): perl-ExtUtils-Command-7.62-479.fc35.n 1.2 MB/s | 15 kB 00:00 (41/105): perl-ExtUtils-Constant-0.25-481.fc35. 3.9 MB/s | 56 kB 00:00 (42/105): perl-ExtUtils-Embed-1.35-481.fc35.noa 1.9 MB/s | 27 kB 00:00 (43/105): perl-Encode-3.11-479.fc35.i686.rpm 26 MB/s | 1.2 MB 00:00 (44/105): perl-ExtUtils-Install-2.20-478.fc35.n 3.0 MB/s | 44 kB 00:00 (45/105): perl-ExtUtils-MakeMaker-7.62-479.fc35 16 MB/s | 289 kB 00:00 (46/105): perl-ExtUtils-Manifest-1.73-478.fc35. 2.7 MB/s | 34 kB 00:00 (47/105): perl-Fcntl-1.14-481.fc35.i686.rpm 2.3 MB/s | 30 kB 00:00 (48/105): perl-File-Basename-2.85-481.fc35.noar 2.3 MB/s | 26 kB 00:00 (49/105): perl-File-Compare-1.100.600-481.fc35. 1.7 MB/s | 22 kB 00:00 (50/105): perl-ExtUtils-ParseXS-3.43-478.fc35.n 5.9 MB/s | 182 kB 00:00 (51/105): perl-File-Copy-2.35-481.fc35.noarch.r 2.0 MB/s | 29 kB 00:00 (52/105): perl-File-Find-1.39-481.fc35.noarch.r 3.1 MB/s | 35 kB 00:00 (53/105): perl-File-Temp-0.231.100-478.fc35.noa 4.6 MB/s | 59 kB 00:00 (54/105): perl-File-Path-2.18-478.fc35.noarch.r 2.5 MB/s | 35 kB 00:00 (55/105): perl-File-stat-1.09-481.fc35.noarch.r 2.6 MB/s | 26 kB 00:00 (56/105): perl-FindBin-1.52-481.fc35.noarch.rpm 1.9 MB/s | 23 kB 00:00 (57/105): perl-Getopt-Long-2.52-478.fc35.noarch 4.6 MB/s | 60 kB 00:00 (58/105): perl-Getopt-Std-1.13-481.fc35.noarch. 2.1 MB/s | 25 kB 00:00 (59/105): perl-HTTP-Tiny-0.078-1.fc35.noarch.rp 4.4 MB/s | 55 kB 00:00 (60/105): perl-IO-1.46-481.fc35.i686.rpm 7.4 MB/s | 97 kB 00:00 (61/105): perl-IPC-Open3-1.21-481.fc35.noarch.r 3.1 MB/s | 32 kB 00:00 (62/105): perl-MIME-Base64-3.16-478.fc35.i686.r 2.4 MB/s | 30 kB 00:00 (63/105): perl-POSIX-1.97-481.fc35.i686.rpm 8.3 MB/s | 110 kB 00:00 (64/105): perl-PathTools-3.80-478.fc35.i686.rpm 6.9 MB/s | 85 kB 00:00 (65/105): perl-Pod-Escapes-1.07-478.fc35.noarch 1.7 MB/s | 20 kB 00:00 (66/105): perl-Pod-Perldoc-3.28.01-479.fc35.noa 5.7 MB/s | 84 kB 00:00 (67/105): perl-Pod-Simple-3.43-2.fc35.noarch.rp 15 MB/s | 215 kB 00:00 (68/105): perl-Pod-Usage-2.01-478.fc35.noarch.r 3.3 MB/s | 40 kB 00:00 (69/105): perl-SelectSaver-1.02-481.fc35.noarch 1.9 MB/s | 21 kB 00:00 (70/105): perl-Scalar-List-Utils-1.56-461.fc35. 5.6 MB/s | 74 kB 00:00 (71/105): perl-Socket-2.032-2.fc35.i686.rpm 4.3 MB/s | 56 kB 00:00 (72/105): perl-Storable-3.23-478.fc35.i686.rpm 8.4 MB/s | 97 kB 00:00 (73/105): perl-Symbol-1.09-481.fc35.noarch.rpm 1.9 MB/s | 23 kB 00:00 (74/105): perl-Term-Cap-1.17-478.fc35.noarch.rp 2.2 MB/s | 22 kB 00:00 (75/105): perl-Term-ANSIColor-5.01-479.fc35.noa 3.5 MB/s | 48 kB 00:00 (76/105): perl-Test-Harness-3.43-479.fc35.noarc 15 MB/s | 267 kB 00:00 (77/105): perl-Text-Tabs+Wrap-2021.0726-1.fc35. 2.1 MB/s | 22 kB 00:00 (78/105): perl-Text-ParseWords-3.30-478.fc35.no 1.3 MB/s | 16 kB 00:00 (79/105): perl-Time-Local-1.300-478.fc35.noarch 2.9 MB/s | 33 kB 00:00 (80/105): perl-base-2.27-481.fc35.noarch.rpm 1.9 MB/s | 25 kB 00:00 (81/105): perl-Thread-Queue-3.14-478.fc35.noarc 1.4 MB/s | 21 kB 00:00 (82/105): perl-constant-1.33-479.fc35.noarch.rp 2.1 MB/s | 23 kB 00:00 (83/105): perl-if-0.60.900-481.fc35.noarch.rpm 1.9 MB/s | 23 kB 00:00 (84/105): perl-interpreter-5.34.0-481.fc35.i686 6.4 MB/s | 80 kB 00:00 (85/105): perl-lib-0.65-481.fc35.i686.rpm 1.9 MB/s | 24 kB 00:00 (86/105): perl-devel-5.34.0-481.fc35.i686.rpm 24 MB/s | 680 kB 00:00 (87/105): perl-locale-1.10-481.fc35.noarch.rpm 1.9 MB/s | 23 kB 00:00 (88/105): perl-mro-1.25-481.fc35.i686.rpm 3.0 MB/s | 38 kB 00:00 (89/105): perl-overload-1.33-481.fc35.noarch.rp 4.2 MB/s | 55 kB 00:00 (90/105): perl-overloading-0.02-481.fc35.noarch 1.7 MB/s | 22 kB 00:00 (91/105): perl-parent-0.238-478.fc35.noarch.rpm 1.1 MB/s | 14 kB 00:00 (92/105): perl-podlators-4.14-478.fc35.noarch.r 8.1 MB/s | 111 kB 00:00 (93/105): perl-subs-1.04-481.fc35.noarch.rpm 1.7 MB/s | 21 kB 00:00 (94/105): perl-threads-2.26-448.fc35.i686.rpm 3.7 MB/s | 59 kB 00:00 (95/105): perl-threads-shared-1.62-478.fc35.i68 3.0 MB/s | 44 kB 00:00 (96/105): perl-vars-1.05-481.fc35.noarch.rpm 1.5 MB/s | 22 kB 00:00 (97/105): perl-libs-5.34.0-481.fc35.i686.rpm 26 MB/s | 2.2 MB 00:00 (98/105): perl-version-0.99.29-4.fc35.i686.rpm 4.4 MB/s | 63 kB 00:00 (99/105): python3-3.10.0~rc1-1.fc35.i686.rpm 1.7 MB/s | 25 kB 00:00 (100/105): python-setuptools-wheel-57.4.0-1.fc3 20 MB/s | 505 kB 00:00 (101/105): python-pip-wheel-21.1.3-2.fc35.noarc 37 MB/s | 1.3 MB 00:00 (102/105): python3-pyparsing-2.4.7-9.fc35.noarc 9.2 MB/s | 151 kB 00:00 (103/105): systemtap-sdt-devel-4.6~pre16262021g 3.9 MB/s | 71 kB 00:00 (104/105): zlib-devel-1.2.11-30.fc35.i686.rpm 2.7 MB/s | 44 kB 00:00 (105/105): python3-libs-3.10.0~rc1-1.fc35.i686. 36 MB/s | 7.5 MB 00:00 -------------------------------------------------------------------------------- Total 53 MB/s | 74 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.2.1-3.fc35.i686 1/105 Installing : htslib-1.13-1.fc35.i686 2/105 Installing : python-setuptools-wheel-57.4.0-1.fc35.noarch 3/105 Installing : python-pip-wheel-21.1.3-2.fc35.noarch 4/105 Installing : kernel-headers-5.14.0-0.rc4.git0.1.fc35.i686 5/105 Installing : glibc-headers-x86-2.34-1.fc35.noarch 6/105 Installing : libxcrypt-devel-4.4.24-1.fc35.i686 7/105 Installing : glibc-devel-2.34-1.fc35.i686 8/105 Installing : emacs-filesystem-1:27.2-9.fc35.noarch 9/105 Installing : annobin-docs-9.83-1.fc35.noarch 10/105 Installing : cpp-11.2.1-1.fc35.i686 11/105 Installing : ncurses-6.2-8.20210508.fc35.i686 12/105 Installing : mpdecimal-2.5.1-2.fc35.i686 13/105 Installing : m4-1.4.19-2.fc35.i686 14/105 Installing : libubsan-11.2.1-1.fc35.i686 15/105 Installing : libtool-ltdl-2.4.6-42.fc35.i686 16/105 Installing : libatomic-11.2.1-1.fc35.i686 17/105 Installing : libasan-11.2.1-1.fc35.i686 18/105 Installing : gsl-2.6-5.fc35.i686 19/105 Running scriptlet: groff-base-1.22.4-8.fc35.i686 20/105 Installing : groff-base-1.22.4-8.fc35.i686 20/105 Running scriptlet: groff-base-1.22.4-8.fc35.i686 20/105 Installing : perl-Text-Tabs+Wrap-2021.0726-1.fc35.noarch 21/105 Installing : perl-if-0.60.900-481.fc35.noarch 22/105 Installing : perl-Time-Local-2:1.300-478.fc35.noarch 23/105 Installing : perl-File-Path-2.18-478.fc35.noarch 24/105 Installing : perl-Pod-Escapes-1:1.07-478.fc35.noarch 25/105 Installing : perl-Class-Struct-0.66-481.fc35.noarch 26/105 Installing : perl-POSIX-1.97-481.fc35.i686 27/105 Installing : perl-Term-ANSIColor-5.01-479.fc35.noarch 28/105 Installing : perl-IPC-Open3-1.21-481.fc35.noarch 29/105 Installing : perl-HTTP-Tiny-0.078-1.fc35.noarch 30/105 Installing : perl-subs-1.04-481.fc35.noarch 31/105 Installing : perl-File-Temp-1:0.231.100-478.fc35.noarch 32/105 Installing : perl-Term-Cap-1.17-478.fc35.noarch 33/105 Installing : perl-Pod-Simple-1:3.43-2.fc35.noarch 34/105 Installing : perl-Socket-4:2.032-2.fc35.i686 35/105 Installing : perl-SelectSaver-1.02-481.fc35.noarch 36/105 Installing : perl-Symbol-1.09-481.fc35.noarch 37/105 Installing : perl-File-stat-1.09-481.fc35.noarch 38/105 Installing : perl-podlators-1:4.14-478.fc35.noarch 39/105 Installing : perl-Pod-Perldoc-3.28.01-479.fc35.noarch 40/105 Installing : perl-Fcntl-1.14-481.fc35.i686 41/105 Installing : perl-Text-ParseWords-3.30-478.fc35.noarch 42/105 Installing : perl-mro-1.25-481.fc35.i686 43/105 Installing : perl-IO-1.46-481.fc35.i686 44/105 Installing : perl-overloading-0.02-481.fc35.noarch 45/105 Installing : perl-Pod-Usage-4:2.01-478.fc35.noarch 46/105 Installing : perl-Errno-1.33-481.fc35.i686 47/105 Installing : perl-File-Basename-2.85-481.fc35.noarch 48/105 Installing : perl-Getopt-Std-1.13-481.fc35.noarch 49/105 Installing : perl-MIME-Base64-3.16-478.fc35.i686 50/105 Installing : perl-Scalar-List-Utils-5:1.56-461.fc35.i686 51/105 Installing : perl-constant-1.33-479.fc35.noarch 52/105 Installing : perl-Storable-1:3.23-478.fc35.i686 53/105 Installing : perl-overload-1.33-481.fc35.noarch 54/105 Installing : perl-parent-1:0.238-478.fc35.noarch 55/105 Installing : perl-vars-1.05-481.fc35.noarch 56/105 Installing : perl-Getopt-Long-1:2.52-478.fc35.noarch 57/105 Installing : perl-DynaLoader-1.50-481.fc35.i686 58/105 Installing : perl-Carp-1.52-478.fc35.noarch 59/105 Installing : perl-Exporter-5.76-479.fc35.noarch 60/105 Installing : perl-PathTools-3.80-478.fc35.i686 61/105 Installing : perl-Encode-4:3.11-479.fc35.i686 62/105 Installing : perl-libs-4:5.34.0-481.fc35.i686 63/105 Installing : perl-interpreter-4:5.34.0-481.fc35.i686 64/105 Installing : perl-File-Find-1.39-481.fc35.noarch 65/105 Installing : perl-File-Copy-2.35-481.fc35.noarch 66/105 Installing : perl-File-Compare-1.100.600-481.fc35.noarch 67/105 Installing : perl-Data-Dumper-2.183-2.fc35.i686 68/105 Installing : perl-B-1.82-481.fc35.i686 69/105 Installing : perl-ExtUtils-ParseXS-1:3.43-478.fc35.noarch 70/105 Installing : perl-threads-1:2.26-448.fc35.i686 71/105 Installing : autoconf-2.69-37.fc35.noarch 72/105 Installing : perl-ExtUtils-Constant-0.25-481.fc35.noarch 73/105 Installing : perl-ExtUtils-Command-2:7.62-479.fc35.noarch 74/105 Installing : perl-ExtUtils-Manifest-1:1.73-478.fc35.noarch 75/105 Installing : perl-AutoSplit-5.74-481.fc35.noarch 76/105 Installing : perl-Benchmark-1.23-481.fc35.noarch 77/105 Installing : perl-base-2.27-481.fc35.noarch 78/105 Installing : perl-Test-Harness-1:3.43-479.fc35.noarch 79/105 Installing : perl-lib-0.65-481.fc35.i686 80/105 Installing : perl-locale-1.10-481.fc35.noarch 81/105 Installing : perl-version-8:0.99.29-4.fc35.i686 82/105 Installing : perl-threads-shared-1.62-478.fc35.i686 83/105 Installing : perl-Thread-Queue-3.14-478.fc35.noarch 84/105 Installing : automake-1.16.2-5.fc35.noarch 85/105 Installing : perl-Devel-PPPort-3.63-2.fc35.i686 86/105 Installing : gc-8.0.4-6.fc35.i686 87/105 Installing : guile22-2.2.7-3.fc35.i686 88/105 Installing : make-1:4.3-6.fc35.i686 89/105 Installing : gcc-11.2.1-1.fc35.i686 90/105 Installing : expat-2.4.1-2.fc35.i686 91/105 Installing : gsl-devel-2.6-5.fc35.i686 92/105 Installing : perl-FindBin-1.52-481.fc35.noarch 93/105 Installing : htslib-devel-1.13-1.fc35.i686 94/105 Installing : zlib-devel-1.2.11-30.fc35.i686 95/105 Installing : python3-3.10.0~rc1-1.fc35.i686 96/105 Installing : python3-libs-3.10.0~rc1-1.fc35.i686 97/105 Installing : python3-pyparsing-2.4.7-9.fc35.noarch 98/105 Installing : systemtap-sdt-devel-4.6~pre16262021g84ef6bd9-2.f 99/105 Installing : perl-devel-4:5.34.0-481.fc35.i686 100/105 Installing : perl-ExtUtils-Install-2.20-478.fc35.noarch 101/105 Installing : perl-ExtUtils-MakeMaker-2:7.62-479.fc35.noarch 102/105 Installing : perl-ExtUtils-Embed-1.35-481.fc35.noarch 103/105 Installing : annobin-plugin-gcc-9.83-1.fc35.i686 104/105 Installing : htslib-tools-1.13-1.fc35.i686 105/105 Running scriptlet: htslib-tools-1.13-1.fc35.i686 105/105 Verifying : htslib-1.13-1.fc35.i686 1/105 Verifying : htslib-devel-1.13-1.fc35.i686 2/105 Verifying : htslib-tools-1.13-1.fc35.i686 3/105 Verifying : annobin-docs-9.83-1.fc35.noarch 4/105 Verifying : annobin-plugin-gcc-9.83-1.fc35.i686 5/105 Verifying : autoconf-2.69-37.fc35.noarch 6/105 Verifying : automake-1.16.2-5.fc35.noarch 7/105 Verifying : cpp-11.2.1-1.fc35.i686 8/105 Verifying : emacs-filesystem-1:27.2-9.fc35.noarch 9/105 Verifying : expat-2.4.1-2.fc35.i686 10/105 Verifying : gc-8.0.4-6.fc35.i686 11/105 Verifying : gcc-11.2.1-1.fc35.i686 12/105 Verifying : glibc-devel-2.34-1.fc35.i686 13/105 Verifying : glibc-headers-x86-2.34-1.fc35.noarch 14/105 Verifying : groff-base-1.22.4-8.fc35.i686 15/105 Verifying : gsl-2.6-5.fc35.i686 16/105 Verifying : gsl-devel-2.6-5.fc35.i686 17/105 Verifying : guile22-2.2.7-3.fc35.i686 18/105 Verifying : kernel-headers-5.14.0-0.rc4.git0.1.fc35.i686 19/105 Verifying : libasan-11.2.1-1.fc35.i686 20/105 Verifying : libatomic-11.2.1-1.fc35.i686 21/105 Verifying : libmpc-1.2.1-3.fc35.i686 22/105 Verifying : libtool-ltdl-2.4.6-42.fc35.i686 23/105 Verifying : libubsan-11.2.1-1.fc35.i686 24/105 Verifying : libxcrypt-devel-4.4.24-1.fc35.i686 25/105 Verifying : m4-1.4.19-2.fc35.i686 26/105 Verifying : make-1:4.3-6.fc35.i686 27/105 Verifying : mpdecimal-2.5.1-2.fc35.i686 28/105 Verifying : ncurses-6.2-8.20210508.fc35.i686 29/105 Verifying : perl-AutoSplit-5.74-481.fc35.noarch 30/105 Verifying : perl-B-1.82-481.fc35.i686 31/105 Verifying : perl-Benchmark-1.23-481.fc35.noarch 32/105 Verifying : perl-Carp-1.52-478.fc35.noarch 33/105 Verifying : perl-Class-Struct-0.66-481.fc35.noarch 34/105 Verifying : perl-Data-Dumper-2.183-2.fc35.i686 35/105 Verifying : perl-Devel-PPPort-3.63-2.fc35.i686 36/105 Verifying : perl-DynaLoader-1.50-481.fc35.i686 37/105 Verifying : perl-Encode-4:3.11-479.fc35.i686 38/105 Verifying : perl-Errno-1.33-481.fc35.i686 39/105 Verifying : perl-Exporter-5.76-479.fc35.noarch 40/105 Verifying : perl-ExtUtils-Command-2:7.62-479.fc35.noarch 41/105 Verifying : perl-ExtUtils-Constant-0.25-481.fc35.noarch 42/105 Verifying : perl-ExtUtils-Embed-1.35-481.fc35.noarch 43/105 Verifying : perl-ExtUtils-Install-2.20-478.fc35.noarch 44/105 Verifying : perl-ExtUtils-MakeMaker-2:7.62-479.fc35.noarch 45/105 Verifying : perl-ExtUtils-Manifest-1:1.73-478.fc35.noarch 46/105 Verifying : perl-ExtUtils-ParseXS-1:3.43-478.fc35.noarch 47/105 Verifying : perl-Fcntl-1.14-481.fc35.i686 48/105 Verifying : perl-File-Basename-2.85-481.fc35.noarch 49/105 Verifying : perl-File-Compare-1.100.600-481.fc35.noarch 50/105 Verifying : perl-File-Copy-2.35-481.fc35.noarch 51/105 Verifying : perl-File-Find-1.39-481.fc35.noarch 52/105 Verifying : perl-File-Path-2.18-478.fc35.noarch 53/105 Verifying : perl-File-Temp-1:0.231.100-478.fc35.noarch 54/105 Verifying : perl-File-stat-1.09-481.fc35.noarch 55/105 Verifying : perl-FindBin-1.52-481.fc35.noarch 56/105 Verifying : perl-Getopt-Long-1:2.52-478.fc35.noarch 57/105 Verifying : perl-Getopt-Std-1.13-481.fc35.noarch 58/105 Verifying : perl-HTTP-Tiny-0.078-1.fc35.noarch 59/105 Verifying : perl-IO-1.46-481.fc35.i686 60/105 Verifying : perl-IPC-Open3-1.21-481.fc35.noarch 61/105 Verifying : perl-MIME-Base64-3.16-478.fc35.i686 62/105 Verifying : perl-POSIX-1.97-481.fc35.i686 63/105 Verifying : perl-PathTools-3.80-478.fc35.i686 64/105 Verifying : perl-Pod-Escapes-1:1.07-478.fc35.noarch 65/105 Verifying : perl-Pod-Perldoc-3.28.01-479.fc35.noarch 66/105 Verifying : perl-Pod-Simple-1:3.43-2.fc35.noarch 67/105 Verifying : perl-Pod-Usage-4:2.01-478.fc35.noarch 68/105 Verifying : perl-Scalar-List-Utils-5:1.56-461.fc35.i686 69/105 Verifying : perl-SelectSaver-1.02-481.fc35.noarch 70/105 Verifying : perl-Socket-4:2.032-2.fc35.i686 71/105 Verifying : perl-Storable-1:3.23-478.fc35.i686 72/105 Verifying : perl-Symbol-1.09-481.fc35.noarch 73/105 Verifying : perl-Term-ANSIColor-5.01-479.fc35.noarch 74/105 Verifying : perl-Term-Cap-1.17-478.fc35.noarch 75/105 Verifying : perl-Test-Harness-1:3.43-479.fc35.noarch 76/105 Verifying : perl-Text-ParseWords-3.30-478.fc35.noarch 77/105 Verifying : perl-Text-Tabs+Wrap-2021.0726-1.fc35.noarch 78/105 Verifying : perl-Thread-Queue-3.14-478.fc35.noarch 79/105 Verifying : perl-Time-Local-2:1.300-478.fc35.noarch 80/105 Verifying : perl-base-2.27-481.fc35.noarch 81/105 Verifying : perl-constant-1.33-479.fc35.noarch 82/105 Verifying : perl-devel-4:5.34.0-481.fc35.i686 83/105 Verifying : perl-if-0.60.900-481.fc35.noarch 84/105 Verifying : perl-interpreter-4:5.34.0-481.fc35.i686 85/105 Verifying : perl-lib-0.65-481.fc35.i686 86/105 Verifying : perl-libs-4:5.34.0-481.fc35.i686 87/105 Verifying : perl-locale-1.10-481.fc35.noarch 88/105 Verifying : perl-mro-1.25-481.fc35.i686 89/105 Verifying : perl-overload-1.33-481.fc35.noarch 90/105 Verifying : perl-overloading-0.02-481.fc35.noarch 91/105 Verifying : perl-parent-1:0.238-478.fc35.noarch 92/105 Verifying : perl-podlators-1:4.14-478.fc35.noarch 93/105 Verifying : perl-subs-1.04-481.fc35.noarch 94/105 Verifying : perl-threads-1:2.26-448.fc35.i686 95/105 Verifying : perl-threads-shared-1.62-478.fc35.i686 96/105 Verifying : perl-vars-1.05-481.fc35.noarch 97/105 Verifying : perl-version-8:0.99.29-4.fc35.i686 98/105 Verifying : python-pip-wheel-21.1.3-2.fc35.noarch 99/105 Verifying : python-setuptools-wheel-57.4.0-1.fc35.noarch 100/105 Verifying : python3-3.10.0~rc1-1.fc35.i686 101/105 Verifying : python3-libs-3.10.0~rc1-1.fc35.i686 102/105 Verifying : python3-pyparsing-2.4.7-9.fc35.noarch 103/105 Verifying : systemtap-sdt-devel-4.6~pre16262021g84ef6bd9-2.f 104/105 Verifying : zlib-devel-1.2.11-30.fc35.i686 105/105 Installed: annobin-docs-9.83-1.fc35.noarch annobin-plugin-gcc-9.83-1.fc35.i686 autoconf-2.69-37.fc35.noarch automake-1.16.2-5.fc35.noarch cpp-11.2.1-1.fc35.i686 emacs-filesystem-1:27.2-9.fc35.noarch expat-2.4.1-2.fc35.i686 gc-8.0.4-6.fc35.i686 gcc-11.2.1-1.fc35.i686 glibc-devel-2.34-1.fc35.i686 glibc-headers-x86-2.34-1.fc35.noarch groff-base-1.22.4-8.fc35.i686 gsl-2.6-5.fc35.i686 gsl-devel-2.6-5.fc35.i686 guile22-2.2.7-3.fc35.i686 htslib-1.13-1.fc35.i686 htslib-devel-1.13-1.fc35.i686 htslib-tools-1.13-1.fc35.i686 kernel-headers-5.14.0-0.rc4.git0.1.fc35.i686 libasan-11.2.1-1.fc35.i686 libatomic-11.2.1-1.fc35.i686 libmpc-1.2.1-3.fc35.i686 libtool-ltdl-2.4.6-42.fc35.i686 libubsan-11.2.1-1.fc35.i686 libxcrypt-devel-4.4.24-1.fc35.i686 m4-1.4.19-2.fc35.i686 make-1:4.3-6.fc35.i686 mpdecimal-2.5.1-2.fc35.i686 ncurses-6.2-8.20210508.fc35.i686 perl-AutoSplit-5.74-481.fc35.noarch perl-B-1.82-481.fc35.i686 perl-Benchmark-1.23-481.fc35.noarch perl-Carp-1.52-478.fc35.noarch perl-Class-Struct-0.66-481.fc35.noarch perl-Data-Dumper-2.183-2.fc35.i686 perl-Devel-PPPort-3.63-2.fc35.i686 perl-DynaLoader-1.50-481.fc35.i686 perl-Encode-4:3.11-479.fc35.i686 perl-Errno-1.33-481.fc35.i686 perl-Exporter-5.76-479.fc35.noarch perl-ExtUtils-Command-2:7.62-479.fc35.noarch perl-ExtUtils-Constant-0.25-481.fc35.noarch perl-ExtUtils-Embed-1.35-481.fc35.noarch perl-ExtUtils-Install-2.20-478.fc35.noarch perl-ExtUtils-MakeMaker-2:7.62-479.fc35.noarch perl-ExtUtils-Manifest-1:1.73-478.fc35.noarch perl-ExtUtils-ParseXS-1:3.43-478.fc35.noarch perl-Fcntl-1.14-481.fc35.i686 perl-File-Basename-2.85-481.fc35.noarch perl-File-Compare-1.100.600-481.fc35.noarch perl-File-Copy-2.35-481.fc35.noarch perl-File-Find-1.39-481.fc35.noarch perl-File-Path-2.18-478.fc35.noarch perl-File-Temp-1:0.231.100-478.fc35.noarch perl-File-stat-1.09-481.fc35.noarch perl-FindBin-1.52-481.fc35.noarch perl-Getopt-Long-1:2.52-478.fc35.noarch perl-Getopt-Std-1.13-481.fc35.noarch perl-HTTP-Tiny-0.078-1.fc35.noarch perl-IO-1.46-481.fc35.i686 perl-IPC-Open3-1.21-481.fc35.noarch perl-MIME-Base64-3.16-478.fc35.i686 perl-POSIX-1.97-481.fc35.i686 perl-PathTools-3.80-478.fc35.i686 perl-Pod-Escapes-1:1.07-478.fc35.noarch perl-Pod-Perldoc-3.28.01-479.fc35.noarch perl-Pod-Simple-1:3.43-2.fc35.noarch perl-Pod-Usage-4:2.01-478.fc35.noarch perl-Scalar-List-Utils-5:1.56-461.fc35.i686 perl-SelectSaver-1.02-481.fc35.noarch perl-Socket-4:2.032-2.fc35.i686 perl-Storable-1:3.23-478.fc35.i686 perl-Symbol-1.09-481.fc35.noarch perl-Term-ANSIColor-5.01-479.fc35.noarch perl-Term-Cap-1.17-478.fc35.noarch perl-Test-Harness-1:3.43-479.fc35.noarch perl-Text-ParseWords-3.30-478.fc35.noarch perl-Text-Tabs+Wrap-2021.0726-1.fc35.noarch perl-Thread-Queue-3.14-478.fc35.noarch perl-Time-Local-2:1.300-478.fc35.noarch perl-base-2.27-481.fc35.noarch perl-constant-1.33-479.fc35.noarch perl-devel-4:5.34.0-481.fc35.i686 perl-if-0.60.900-481.fc35.noarch perl-interpreter-4:5.34.0-481.fc35.i686 perl-lib-0.65-481.fc35.i686 perl-libs-4:5.34.0-481.fc35.i686 perl-locale-1.10-481.fc35.noarch perl-mro-1.25-481.fc35.i686 perl-overload-1.33-481.fc35.noarch perl-overloading-0.02-481.fc35.noarch perl-parent-1:0.238-478.fc35.noarch perl-podlators-1:4.14-478.fc35.noarch perl-subs-1.04-481.fc35.noarch perl-threads-1:2.26-448.fc35.i686 perl-threads-shared-1.62-478.fc35.i686 perl-vars-1.05-481.fc35.noarch perl-version-8:0.99.29-4.fc35.i686 python-pip-wheel-21.1.3-2.fc35.noarch python-setuptools-wheel-57.4.0-1.fc35.noarch python3-3.10.0~rc1-1.fc35.i686 python3-libs-3.10.0~rc1-1.fc35.i686 python3-pyparsing-2.4.7-9.fc35.noarch systemtap-sdt-devel-4.6~pre16262021g84ef6bd9-2.fc35.i686 zlib-devel-1.2.11-30.fc35.i686 Complete! Finish: build setup for bcftools-1.13-1.fc35.src.rpm Start: rpmbuild bcftools-1.13-1.fc35.src.rpm Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1626998400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.0PEPYh + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bcftools-1.13 + /usr/bin/bzip2 -dc /builddir/build/SOURCES/bcftools-1.13.tar.bz2 + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd bcftools-1.13 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + sed -i '1s|/usr/bin/env perl|/usr/bin/perl|' misc/color-chrs.pl misc/demo-flt.pl misc/run-roh.pl misc/vcfutils.pl misc/plot-vcfstats + sed -i '1s|/usr/bin/env python3\{0,1\}|/usr/bin/python3|' misc/gff2gff.py misc/guess-ploidy.py misc/plot-roh.py + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.cEgg5S + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.13 + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + 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-1.13/configure + diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure + mv ./htslib-1.13/configure.backup ./htslib-1.13/configure + /usr/bin/sed -r --in-place=.backup 's/^char $\*f$ ;/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.13/configure + diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure + mv ./htslib-1.13/configure.backup ./htslib-1.13/configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 ;/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.13/configure + diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure --- ./htslib-1.13/configure.backup 2021-07-07 18:06:34.000000000 +0000 +++ ./htslib-1.13/configure 2021-08-08 18:40:00.561019242 +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-1.13/configure + diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure + mv ./htslib-1.13/configure.backup ./htslib-1.13/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-1.13/configure + diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure + mv ./htslib-1.13/configure.backup ./htslib-1.13/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 + ./configure --build=i686-redhat-linux-gnu --host=i686-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/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' --prefix=/usr --with-htslib=system --enable-perl-filters --enable-libgsl '--with-bcf-plugin-path=/usr/local/libexec/bcftools:$(plugindir)' checking for i686-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... 64 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 "1.13"' > 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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/lib/perl5/CORE -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o 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 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fstack-protector-strong -L/usr/local/lib -L/usr/lib/perl5/CORE -lperl -lpthread -lresolv -ldl -lm -lcrypt -lutil -lc -lpthread vcfcnv.c:1132:5: warning: type of 'read_AF' does not match original declaration [-Wlto-type-mismatch] 1132 | int read_AF(bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq); | ^ vcfroh.c:661:5: note: type mismatch in parameter 4 661 | int read_AF(args_t *args, bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq) | ^ vcfroh.c:661:5: note: 'read_AF' was previously declared here + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.VPxxaD + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386 ++ dirname /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386 + cd bcftools-1.13 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/bin /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/share/man/man1 /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools /usr/bin/install -p bcftools /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/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-1.13-1.fc35.i386/usr/bin /usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/share/man/man1 /usr/bin/install -p plugins/*.so /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.13-1.fc35 --unique-debug-suffix -1.13-1.fc35.i386 --unique-debug-src-base bcftools-1.13-1.fc35.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bcftools-1.13 extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/bin/bcftools extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/GTisec.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/GTsubset.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/ad-bias.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/add-variantkey.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/af-dist.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/allele-length.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/check-ploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/check-sparsity.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/color-chrs.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/contrast.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/counts.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/dosage.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/fill-AN-AC.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/fill-from-fasta.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/fill-tags.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/fixploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/fixref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/frameshifts.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/guess-ploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/gvcfz.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/impute-info.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/indel-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/isecGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/mendelian.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/missing2ref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/parental-origin.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/prune.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/remove-overlaps.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/scatter.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/setGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/smpl-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/split-vep.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/split.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/tag2tag.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/trio-dnm2.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/trio-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/trio-switch-rate.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/libexec/bcftools/variantkey-hex.so original debug info size: 5388kB, size after compression: 4644kB /usr/bin/sepdebugcrcfix: Updated 39 CRC32s, 0 CRC32s did match. 5215 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/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.WSg2dk + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.13 + ldd bcftools + grep -E '/lib(64)?/libhts\.so\.' libhts.so.3 => /lib/libhts.so.3 (0xf7dad000) + 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/MM8SwH8Pi0/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/MM8SwH8Pi0/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/MM8SwH8Pi0/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/MM8SwH8Pi0/merge.a.bcf 1:3000151-3000151 .. ok test_index: /builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/MM8SwH8Pi0/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/MM8SwH8Pi0/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/MM8SwH8Pi0/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/MM8SwH8Pi0/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/MM8SwH8Pi0/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/MM8SwH8Pi0/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/MM8SwH8Pi0/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/MM8SwH8Pi0/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/MM8SwH8Pi0/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/MM8SwH8Pi0/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -s /tmp/MM8SwH8Pi0/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -s /tmp/MM8SwH8Pi0/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -s /tmp/MM8SwH8Pi0/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/MM8SwH8Pi0/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/MM8SwH8Pi0/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/MM8SwH8Pi0/idx.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/MM8SwH8Pi0/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/MM8SwH8Pi0/idx.bcf.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -s /tmp/MM8SwH8Pi0/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -s /tmp/MM8SwH8Pi0/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -s /tmp/MM8SwH8Pi0/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/MM8SwH8Pi0/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/MM8SwH8Pi0/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/MM8SwH8Pi0/empty.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/MM8SwH8Pi0/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/MM8SwH8Pi0/empty.bcf.csi .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.13/bcftools stats -s - /tmp/MM8SwH8Pi0/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /builddir/build/BUILD/bcftools-1.13/misc/plot-vcfstats -m /tmp/MM8SwH8Pi0/check.1.chk /tmp/MM8SwH8Pi0/check.2.chk /tmp/MM8SwH8Pi0/check.3.chk /tmp/MM8SwH8Pi0/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-1.13/bcftools stats -s - /tmp/MM8SwH8Pi0/stats.a.vcf.gz /tmp/MM8SwH8Pi0/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.13/bcftools stats -s B /tmp/MM8SwH8Pi0/stats.a.vcf.gz /tmp/MM8SwH8Pi0/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.13/bcftools stats -s - /tmp/MM8SwH8Pi0/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -n =2 /tmp/MM8SwH8Pi0/isec.a.vcf.gz /tmp/MM8SwH8Pi0/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -n =2 /tmp/MM8SwH8Pi0/isec.a.vcf.gz /tmp/MM8SwH8Pi0/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/MM8SwH8Pi0/isec.a.vcf.gz /tmp/MM8SwH8Pi0/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/MM8SwH8Pi0/isec.a.vcf.gz /tmp/MM8SwH8Pi0/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -n =2 -c both /tmp/MM8SwH8Pi0/isec.a.vcf.gz /tmp/MM8SwH8Pi0/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -n =2 -c both /tmp/MM8SwH8Pi0/isec.a.vcf.gz /tmp/MM8SwH8Pi0/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -n =2 -c any /tmp/MM8SwH8Pi0/isec.a.vcf.gz /tmp/MM8SwH8Pi0/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -n =2 -c any /tmp/MM8SwH8Pi0/isec.a.vcf.gz /tmp/MM8SwH8Pi0/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -C -c any /tmp/MM8SwH8Pi0/isec.a.vcf.gz /tmp/MM8SwH8Pi0/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -C -c any /tmp/MM8SwH8Pi0/isec.a.vcf.gz /tmp/MM8SwH8Pi0/isec.b.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.13/bcftools isec --no-version -T /tmp/MM8SwH8Pi0/isec.tab.gz /tmp/MM8SwH8Pi0/isec.a.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -T /tmp/MM8SwH8Pi0/isec.tab.gz /tmp/MM8SwH8Pi0/isec.a.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/MM8SwH8Pi0/isec-miss.1.1.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.1.2.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/MM8SwH8Pi0/isec-miss.1.1.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.1.2.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -R /builddir/build/BUILD/bcftools-1.13/test/isec-miss.1.regs.txt -n +1 /tmp/MM8SwH8Pi0/isec-miss.1.1.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.1.2.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.13/test/isec-miss.1.regs.txt -n +1 /tmp/MM8SwH8Pi0/isec-miss.1.1.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.1.2.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/MM8SwH8Pi0/isec-miss.2.1.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.2.2.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/MM8SwH8Pi0/isec-miss.2.1.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.2.2.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -R /builddir/build/BUILD/bcftools-1.13/test/isec-miss.1.regs.txt -n +1 /tmp/MM8SwH8Pi0/isec-miss.2.1.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.2.2.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.13/test/isec-miss.1.regs.txt -n +1 /tmp/MM8SwH8Pi0/isec-miss.2.1.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.2.2.vcf.gz /tmp/MM8SwH8Pi0/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -i AF:join /tmp/MM8SwH8Pi0/merge.join.a.vcf.gz /tmp/MM8SwH8Pi0/merge.join.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -i AF:join /tmp/MM8SwH8Pi0/merge.join.a.vcf.gz /tmp/MM8SwH8Pi0/merge.join.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -i AF:join /tmp/MM8SwH8Pi0/merge.join.a.bcf /tmp/MM8SwH8Pi0/merge.join.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -i AF:join /tmp/MM8SwH8Pi0/merge.join.a.bcf /tmp/MM8SwH8Pi0/merge.join.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/MM8SwH8Pi0/merge.LPL.a.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.b.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/MM8SwH8Pi0/merge.LPL.a.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.b.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/MM8SwH8Pi0/merge.LPL.a.bcf /tmp/MM8SwH8Pi0/merge.LPL.b.bcf /tmp/MM8SwH8Pi0/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/MM8SwH8Pi0/merge.LPL.a.bcf /tmp/MM8SwH8Pi0/merge.LPL.b.bcf /tmp/MM8SwH8Pi0/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 1 /tmp/MM8SwH8Pi0/merge.LPL.a.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.b.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 1 /tmp/MM8SwH8Pi0/merge.LPL.a.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.b.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 1 /tmp/MM8SwH8Pi0/merge.LPL.a.bcf /tmp/MM8SwH8Pi0/merge.LPL.b.bcf /tmp/MM8SwH8Pi0/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 1 /tmp/MM8SwH8Pi0/merge.LPL.a.bcf /tmp/MM8SwH8Pi0/merge.LPL.b.bcf /tmp/MM8SwH8Pi0/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 2 /tmp/MM8SwH8Pi0/merge.LPL.a.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.b.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 2 /tmp/MM8SwH8Pi0/merge.LPL.a.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.b.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 2 /tmp/MM8SwH8Pi0/merge.LPL.a.bcf /tmp/MM8SwH8Pi0/merge.LPL.b.bcf /tmp/MM8SwH8Pi0/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 2 /tmp/MM8SwH8Pi0/merge.LPL.a.bcf /tmp/MM8SwH8Pi0/merge.LPL.b.bcf /tmp/MM8SwH8Pi0/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 3 /tmp/MM8SwH8Pi0/merge.LPL.a.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.b.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 3 /tmp/MM8SwH8Pi0/merge.LPL.a.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.b.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 3 /tmp/MM8SwH8Pi0/merge.LPL.a.bcf /tmp/MM8SwH8Pi0/merge.LPL.b.bcf /tmp/MM8SwH8Pi0/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 3 /tmp/MM8SwH8Pi0/merge.LPL.a.bcf /tmp/MM8SwH8Pi0/merge.LPL.b.bcf /tmp/MM8SwH8Pi0/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 4 /tmp/MM8SwH8Pi0/merge.LPL.a.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.b.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 4 /tmp/MM8SwH8Pi0/merge.LPL.a.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.b.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 4 /tmp/MM8SwH8Pi0/merge.LPL.a.bcf /tmp/MM8SwH8Pi0/merge.LPL.b.bcf /tmp/MM8SwH8Pi0/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 4 /tmp/MM8SwH8Pi0/merge.LPL.a.bcf /tmp/MM8SwH8Pi0/merge.LPL.b.bcf /tmp/MM8SwH8Pi0/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 5 /tmp/MM8SwH8Pi0/merge.LPL.a.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.b.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 5 /tmp/MM8SwH8Pi0/merge.LPL.a.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.b.vcf.gz /tmp/MM8SwH8Pi0/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 5 /tmp/MM8SwH8Pi0/merge.LPL.a.bcf /tmp/MM8SwH8Pi0/merge.LPL.b.bcf /tmp/MM8SwH8Pi0/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 5 /tmp/MM8SwH8Pi0/merge.LPL.a.bcf /tmp/MM8SwH8Pi0/merge.LPL.b.bcf /tmp/MM8SwH8Pi0/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/MM8SwH8Pi0/merge.a.vcf.gz /tmp/MM8SwH8Pi0/merge.b.vcf.gz /tmp/MM8SwH8Pi0/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/MM8SwH8Pi0/merge.a.vcf.gz /tmp/MM8SwH8Pi0/merge.b.vcf.gz /tmp/MM8SwH8Pi0/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/MM8SwH8Pi0/merge.a.bcf /tmp/MM8SwH8Pi0/merge.b.bcf /tmp/MM8SwH8Pi0/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/MM8SwH8Pi0/merge.a.bcf /tmp/MM8SwH8Pi0/merge.b.bcf /tmp/MM8SwH8Pi0/merge.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -Fx /tmp/MM8SwH8Pi0/merge.a.vcf.gz /tmp/MM8SwH8Pi0/merge.b.vcf.gz /tmp/MM8SwH8Pi0/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -Fx /tmp/MM8SwH8Pi0/merge.a.vcf.gz /tmp/MM8SwH8Pi0/merge.b.vcf.gz /tmp/MM8SwH8Pi0/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -Fx /tmp/MM8SwH8Pi0/merge.a.bcf /tmp/MM8SwH8Pi0/merge.b.bcf /tmp/MM8SwH8Pi0/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -Fx /tmp/MM8SwH8Pi0/merge.a.bcf /tmp/MM8SwH8Pi0/merge.b.bcf /tmp/MM8SwH8Pi0/merge.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -0 /tmp/MM8SwH8Pi0/merge.a.vcf.gz /tmp/MM8SwH8Pi0/merge.b.vcf.gz /tmp/MM8SwH8Pi0/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -0 /tmp/MM8SwH8Pi0/merge.a.vcf.gz /tmp/MM8SwH8Pi0/merge.b.vcf.gz /tmp/MM8SwH8Pi0/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -0 /tmp/MM8SwH8Pi0/merge.a.bcf /tmp/MM8SwH8Pi0/merge.b.bcf /tmp/MM8SwH8Pi0/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -0 /tmp/MM8SwH8Pi0/merge.a.bcf /tmp/MM8SwH8Pi0/merge.b.bcf /tmp/MM8SwH8Pi0/merge.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m none /tmp/MM8SwH8Pi0/merge.2.a.vcf.gz /tmp/MM8SwH8Pi0/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m none /tmp/MM8SwH8Pi0/merge.2.a.vcf.gz /tmp/MM8SwH8Pi0/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m none /tmp/MM8SwH8Pi0/merge.2.a.bcf /tmp/MM8SwH8Pi0/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m none /tmp/MM8SwH8Pi0/merge.2.a.bcf /tmp/MM8SwH8Pi0/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m both /tmp/MM8SwH8Pi0/merge.2.a.vcf.gz /tmp/MM8SwH8Pi0/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m both /tmp/MM8SwH8Pi0/merge.2.a.vcf.gz /tmp/MM8SwH8Pi0/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m both /tmp/MM8SwH8Pi0/merge.2.a.bcf /tmp/MM8SwH8Pi0/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m both /tmp/MM8SwH8Pi0/merge.2.a.bcf /tmp/MM8SwH8Pi0/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m all /tmp/MM8SwH8Pi0/merge.2.a.vcf.gz /tmp/MM8SwH8Pi0/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m all /tmp/MM8SwH8Pi0/merge.2.a.vcf.gz /tmp/MM8SwH8Pi0/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m all /tmp/MM8SwH8Pi0/merge.2.a.bcf /tmp/MM8SwH8Pi0/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m all /tmp/MM8SwH8Pi0/merge.2.a.bcf /tmp/MM8SwH8Pi0/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/MM8SwH8Pi0/merge.3.a.vcf.gz /tmp/MM8SwH8Pi0/merge.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/MM8SwH8Pi0/merge.3.a.vcf.gz /tmp/MM8SwH8Pi0/merge.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/MM8SwH8Pi0/merge.3.a.bcf /tmp/MM8SwH8Pi0/merge.3.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/MM8SwH8Pi0/merge.3.a.bcf /tmp/MM8SwH8Pi0/merge.3.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m id /tmp/MM8SwH8Pi0/merge.4.a.vcf.gz /tmp/MM8SwH8Pi0/merge.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m id /tmp/MM8SwH8Pi0/merge.4.a.vcf.gz /tmp/MM8SwH8Pi0/merge.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m id /tmp/MM8SwH8Pi0/merge.4.a.bcf /tmp/MM8SwH8Pi0/merge.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m id /tmp/MM8SwH8Pi0/merge.4.a.bcf /tmp/MM8SwH8Pi0/merge.4.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/MM8SwH8Pi0/gvcf.merge.1.vcf.gz /tmp/MM8SwH8Pi0/gvcf.merge.2.vcf.gz /tmp/MM8SwH8Pi0/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/MM8SwH8Pi0/gvcf.merge.1.vcf.gz /tmp/MM8SwH8Pi0/gvcf.merge.2.vcf.gz /tmp/MM8SwH8Pi0/gvcf.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/MM8SwH8Pi0/gvcf.merge.1.bcf /tmp/MM8SwH8Pi0/gvcf.merge.2.bcf /tmp/MM8SwH8Pi0/gvcf.merge.3.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/MM8SwH8Pi0/gvcf.merge.1.bcf /tmp/MM8SwH8Pi0/gvcf.merge.2.bcf /tmp/MM8SwH8Pi0/gvcf.merge.3.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.2.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.2.b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.2.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.2.b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - -i SRC:join /tmp/MM8SwH8Pi0/merge.gvcf.3.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - -i SRC:join /tmp/MM8SwH8Pi0/merge.gvcf.3.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.4.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.4.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.4.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.4.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.4.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version /tmp/MM8SwH8Pi0/merge.5.a.vcf.gz /tmp/MM8SwH8Pi0/merge.5.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob /tmp/MM8SwH8Pi0/merge.5.a.vcf.gz /tmp/MM8SwH8Pi0/merge.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version /tmp/MM8SwH8Pi0/merge.5.a.bcf /tmp/MM8SwH8Pi0/merge.5.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob /tmp/MM8SwH8Pi0/merge.5.a.bcf /tmp/MM8SwH8Pi0/merge.5.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version /tmp/MM8SwH8Pi0/merge.6.a.vcf.gz /tmp/MM8SwH8Pi0/merge.6.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob /tmp/MM8SwH8Pi0/merge.6.a.vcf.gz /tmp/MM8SwH8Pi0/merge.6.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version /tmp/MM8SwH8Pi0/merge.6.a.bcf /tmp/MM8SwH8Pi0/merge.6.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob /tmp/MM8SwH8Pi0/merge.6.a.bcf /tmp/MM8SwH8Pi0/merge.6.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.7.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.7.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.7.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.7.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.7.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.8.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.8.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.8.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/MM8SwH8Pi0/merge.gvcf.8.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.8.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/MM8SwH8Pi0/merge.7.a.vcf.gz /tmp/MM8SwH8Pi0/merge.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/MM8SwH8Pi0/merge.7.a.vcf.gz /tmp/MM8SwH8Pi0/merge.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/MM8SwH8Pi0/merge.7.a.bcf /tmp/MM8SwH8Pi0/merge.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/MM8SwH8Pi0/merge.7.a.bcf /tmp/MM8SwH8Pi0/merge.7.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/MM8SwH8Pi0/merge.gvcf.9a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9c.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/MM8SwH8Pi0/merge.gvcf.9a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9c.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/MM8SwH8Pi0/merge.gvcf.9a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9b.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9c.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9d.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/MM8SwH8Pi0/merge.gvcf.9a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9b.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9c.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/MM8SwH8Pi0/merge.gvcf.9a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9c.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/MM8SwH8Pi0/merge.gvcf.9a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9c.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/MM8SwH8Pi0/merge.gvcf.9a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9b.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9c.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9d.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/MM8SwH8Pi0/merge.gvcf.9a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9b.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9c.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/MM8SwH8Pi0/merge.gvcf.9a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9c.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9d.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/MM8SwH8Pi0/merge.gvcf.9a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9c.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9d.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/MM8SwH8Pi0/merge.gvcf.9a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9b.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9c.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9d.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9e.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/MM8SwH8Pi0/merge.gvcf.9a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9b.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9c.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9d.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/MM8SwH8Pi0/merge.gvcf.9a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9c.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9d.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/MM8SwH8Pi0/merge.gvcf.9a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9c.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9d.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/MM8SwH8Pi0/merge.gvcf.9a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9b.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9c.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9d.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9e.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/MM8SwH8Pi0/merge.gvcf.9a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9b.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9c.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9d.bcf /tmp/MM8SwH8Pi0/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version /tmp/MM8SwH8Pi0/merge.gvcf.10.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob /tmp/MM8SwH8Pi0/merge.gvcf.10.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version /tmp/MM8SwH8Pi0/merge.gvcf.10.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob /tmp/MM8SwH8Pi0/merge.gvcf.10.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -m none /tmp/MM8SwH8Pi0/merge.gvcf.10.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -m none /tmp/MM8SwH8Pi0/merge.gvcf.10.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -m none /tmp/MM8SwH8Pi0/merge.gvcf.10.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -m none /tmp/MM8SwH8Pi0/merge.gvcf.10.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/MM8SwH8Pi0/merge.gvcf.10.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/MM8SwH8Pi0/merge.gvcf.10.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/MM8SwH8Pi0/merge.gvcf.10.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/MM8SwH8Pi0/merge.gvcf.10.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/MM8SwH8Pi0/merge.gvcf.10.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/MM8SwH8Pi0/merge.gvcf.10.a.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/MM8SwH8Pi0/merge.gvcf.10.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/MM8SwH8Pi0/merge.gvcf.10.a.bcf /tmp/MM8SwH8Pi0/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/MM8SwH8Pi0/merge.gvcf.10.b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/MM8SwH8Pi0/merge.gvcf.10.b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/MM8SwH8Pi0/merge.gvcf.10.b.bcf /tmp/MM8SwH8Pi0/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/MM8SwH8Pi0/merge.gvcf.10.b.bcf /tmp/MM8SwH8Pi0/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/MM8SwH8Pi0/merge.gvcf.10.b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/MM8SwH8Pi0/merge.gvcf.10.b.vcf.gz /tmp/MM8SwH8Pi0/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/MM8SwH8Pi0/merge.gvcf.10.b.bcf /tmp/MM8SwH8Pi0/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/MM8SwH8Pi0/merge.gvcf.10.b.bcf /tmp/MM8SwH8Pi0/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version /tmp/MM8SwH8Pi0/merge.noidx.a.vcf.gz /tmp/MM8SwH8Pi0/merge.noidx.b.vcf.gz /tmp/MM8SwH8Pi0/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob /tmp/MM8SwH8Pi0/merge.noidx.a.vcf.gz /tmp/MM8SwH8Pi0/merge.noidx.b.vcf.gz /tmp/MM8SwH8Pi0/merge.noidx.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version /tmp/MM8SwH8Pi0/merge.noidx.a.bcf /tmp/MM8SwH8Pi0/merge.noidx.b.bcf /tmp/MM8SwH8Pi0/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob /tmp/MM8SwH8Pi0/merge.noidx.a.bcf /tmp/MM8SwH8Pi0/merge.noidx.b.bcf /tmp/MM8SwH8Pi0/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --no-index /builddir/build/BUILD/bcftools-1.13/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.13/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.13/test/merge.noidx.c.vcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --no-index /builddir/build/BUILD/bcftools-1.13/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.13/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.13/test/merge.noidx.c.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --no-index /tmp/MM8SwH8Pi0/merge.noidx.a.bcf /tmp/MM8SwH8Pi0/merge.noidx.b.bcf /tmp/MM8SwH8Pi0/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --no-index /tmp/MM8SwH8Pi0/merge.noidx.a.bcf /tmp/MM8SwH8Pi0/merge.noidx.b.bcf /tmp/MM8SwH8Pi0/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/MM8SwH8Pi0/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/MM8SwH8Pi0/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/MM8SwH8Pi0/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools query -f '%RSX\t%VKX\n' /tmp/MM8SwH8Pi0/query.variantkey.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.variantkey.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/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/MM8SwH8Pi0/view.vectors.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/MM8SwH8Pi0/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/MM8SwH8Pi0/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/MM8SwH8Pi0/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/MM8SwH8Pi0/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/MM8SwH8Pi0/query.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/MM8SwH8Pi0/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/MM8SwH8Pi0/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/MM8SwH8Pi0/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/MM8SwH8Pi0/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%LINE' /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%LINE' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/MM8SwH8Pi0/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/MM8SwH8Pi0/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/MM8SwH8Pi0/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/MM8SwH8Pi0/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/MM8SwH8Pi0/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/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/MM8SwH8Pi0/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.13/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-1.13/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/MM8SwH8Pi0/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/MM8SwH8Pi0/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/MM8SwH8Pi0/query.filter.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/MM8SwH8Pi0/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/MM8SwH8Pi0/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/MM8SwH8Pi0/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/MM8SwH8Pi0/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/MM8SwH8Pi0/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/MM8SwH8Pi0/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/MM8SwH8Pi0/query.filter.4.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.4.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.13/test/query.56.out' /tmp/MM8SwH8Pi0/view.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.13/test/query.56.out' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/MM8SwH8Pi0/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/MM8SwH8Pi0/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/MM8SwH8Pi0/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/MM8SwH8Pi0/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/MM8SwH8Pi0/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/MM8SwH8Pi0/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/MM8SwH8Pi0/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/MM8SwH8Pi0/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/MM8SwH8Pi0/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/MM8SwH8Pi0/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/MM8SwH8Pi0/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' /tmp/MM8SwH8Pi0/query.pbinom.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.pbinom.1.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/MM8SwH8Pi0/query.filter.6.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.6.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/MM8SwH8Pi0/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/MM8SwH8Pi0/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/MM8SwH8Pi0/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/MM8SwH8Pi0/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/MM8SwH8Pi0/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/MM8SwH8Pi0/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/MM8SwH8Pi0/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/MM8SwH8Pi0/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/MM8SwH8Pi0/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -cx -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/MM8SwH8Pi0/norm.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -cx -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/MM8SwH8Pi0/norm.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -m- /tmp/MM8SwH8Pi0/norm.split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -m- /tmp/MM8SwH8Pi0/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -m- /tmp/MM8SwH8Pi0/norm.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -m- /tmp/MM8SwH8Pi0/norm.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -m- --force /tmp/MM8SwH8Pi0/norm.split.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -m- --force /tmp/MM8SwH8Pi0/norm.split.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -m- /tmp/MM8SwH8Pi0/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -m- /tmp/MM8SwH8Pi0/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -m- --keep-sum AD /tmp/MM8SwH8Pi0/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -m- --keep-sum AD /tmp/MM8SwH8Pi0/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -m- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/MM8SwH8Pi0/norm.split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -m- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/MM8SwH8Pi0/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -m+ /tmp/MM8SwH8Pi0/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -m+ /tmp/MM8SwH8Pi0/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -m+ /tmp/MM8SwH8Pi0/norm.merge.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -m+ /tmp/MM8SwH8Pi0/norm.merge.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -m+ /tmp/MM8SwH8Pi0/norm.merge.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -m+ /tmp/MM8SwH8Pi0/norm.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -m+ -s /tmp/MM8SwH8Pi0/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -m+ -s /tmp/MM8SwH8Pi0/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -Nc s -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/MM8SwH8Pi0/norm.setref.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -Nc s -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/MM8SwH8Pi0/norm.setref.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/MM8SwH8Pi0/norm.telomere.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/MM8SwH8Pi0/norm.telomere.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -d snps /tmp/MM8SwH8Pi0/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -d snps /tmp/MM8SwH8Pi0/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -d indels /tmp/MM8SwH8Pi0/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -d indels /tmp/MM8SwH8Pi0/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -d both /tmp/MM8SwH8Pi0/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -d both /tmp/MM8SwH8Pi0/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -d all /tmp/MM8SwH8Pi0/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -d all /tmp/MM8SwH8Pi0/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -d none /tmp/MM8SwH8Pi0/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -d none /tmp/MM8SwH8Pi0/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -d exact /tmp/MM8SwH8Pi0/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -d exact /tmp/MM8SwH8Pi0/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -d none /tmp/MM8SwH8Pi0/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -d none /tmp/MM8SwH8Pi0/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -d exact /tmp/MM8SwH8Pi0/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -d exact /tmp/MM8SwH8Pi0/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -d indels /tmp/MM8SwH8Pi0/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -d indels /tmp/MM8SwH8Pi0/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -d any /tmp/MM8SwH8Pi0/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -d any /tmp/MM8SwH8Pi0/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -d both /tmp/MM8SwH8Pi0/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -d both /tmp/MM8SwH8Pi0/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -d snps /tmp/MM8SwH8Pi0/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -d snps /tmp/MM8SwH8Pi0/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -f /builddir/build/BUILD/bcftools-1.13/test/norm.2.fa /tmp/MM8SwH8Pi0/norm.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -f /builddir/build/BUILD/bcftools-1.13/test/norm.2.fa /tmp/MM8SwH8Pi0/norm.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -c s -f /builddir/build/BUILD/bcftools-1.13/test/norm.iupac.fa /tmp/MM8SwH8Pi0/norm.iupac.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -c s -f /builddir/build/BUILD/bcftools-1.13/test/norm.iupac.fa /tmp/MM8SwH8Pi0/norm.iupac.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version -c s -f /builddir/build/BUILD/bcftools-1.13/test/norm.3.fa /tmp/MM8SwH8Pi0/norm.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob -c s -f /builddir/build/BUILD/bcftools-1.13/test/norm.3.fa /tmp/MM8SwH8Pi0/norm.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/MM8SwH8Pi0/atomize.split.1.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/MM8SwH8Pi0/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MM8SwH8Pi0/atomize.split.1.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MM8SwH8Pi0/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/MM8SwH8Pi0/atomize.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/MM8SwH8Pi0/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MM8SwH8Pi0/atomize.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MM8SwH8Pi0/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/MM8SwH8Pi0/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/MM8SwH8Pi0/view.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -f PASS -Xks NA00003 /tmp/MM8SwH8Pi0/view.vcf.gz -r20,Y .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -f PASS -Xks NA00003 /tmp/MM8SwH8Pi0/view.vcf.gz -r20,Y | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -xs NA00003 /tmp/MM8SwH8Pi0/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -xs NA00003 /tmp/MM8SwH8Pi0/view.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/MM8SwH8Pi0/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/MM8SwH8Pi0/view.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -p /tmp/MM8SwH8Pi0/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -p /tmp/MM8SwH8Pi0/view.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -P /tmp/MM8SwH8Pi0/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -P /tmp/MM8SwH8Pi0/view.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/MM8SwH8Pi0/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/MM8SwH8Pi0/view.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -Hu /tmp/MM8SwH8Pi0/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -GVsnps /tmp/MM8SwH8Pi0/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -GVsnps /tmp/MM8SwH8Pi0/view.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/MM8SwH8Pi0/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/MM8SwH8Pi0/view.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -s ^NA00003 /tmp/MM8SwH8Pi0/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -s ^NA00003 /tmp/MM8SwH8Pi0/view.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version /tmp/MM8SwH8Pi0/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -G /tmp/MM8SwH8Pi0/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -G /tmp/MM8SwH8Pi0/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -HG /tmp/MM8SwH8Pi0/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -a /tmp/MM8SwH8Pi0/many.alleles.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -a /tmp/MM8SwH8Pi0/many.alleles.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -asA /tmp/MM8SwH8Pi0/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -asA /tmp/MM8SwH8Pi0/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -asB /tmp/MM8SwH8Pi0/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -asB /tmp/MM8SwH8Pi0/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -asA /tmp/MM8SwH8Pi0/view.vectors.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -asA /tmp/MM8SwH8Pi0/view.vectors.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i'TXT0="text"' /tmp/MM8SwH8Pi0/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.13/test/view.chrs.tab /tmp/MM8SwH8Pi0/view.chrs.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.13/test/view.chrs.tab /tmp/MM8SwH8Pi0/view.chrs.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -i 'POS>=3062917' /tmp/MM8SwH8Pi0/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -i 'POS>=3062917' /tmp/MM8SwH8Pi0/filter.2.vcf.gz 1:3062917-3157410 | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/MM8SwH8Pi0/idx.1.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/MM8SwH8Pi0/idx.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.13/test/idx.2.bed /tmp/MM8SwH8Pi0/idx.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.13/test/idx.3.bed /tmp/MM8SwH8Pi0/idx.3.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.13/test/idx.4.bed /tmp/MM8SwH8Pi0/idx.4.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -Ht 2 /tmp/MM8SwH8Pi0/view-t.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -Ht 3 /tmp/MM8SwH8Pi0/view-t.vcf.gz .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.1.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.1.vcf -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.2.vcf -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.4.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.4.vcf -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.5.vcf -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view -H .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -C5:nonmajor /tmp/MM8SwH8Pi0/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -c6:nonmajor /tmp/MM8SwH8Pi0/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -q0.3:major /tmp/MM8SwH8Pi0/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/MM8SwH8Pi0/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/MM8SwH8Pi0/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/MM8SwH8Pi0/view.filter.annovar.vcf.gz .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mg0 /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mg0 /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.ped /builddir/build/BUILD/bcftools-1.13/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.ped /builddir/build/BUILD/bcftools-1.13/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.13/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.13/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -G /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -G /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.13/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.13/test/mpileup.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.4.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.13/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.13/test/mpileup.cals.1.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.13/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/MM8SwH8Pi0/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.13/test/mpileup.cals.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -cv /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -cv /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.ped /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.ped /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.13/test/call-G.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.13/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/call-G.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.13/test/call-G.2.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.13/test/call-G.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -m /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -m /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.13/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.13/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'ALT="."' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'ALT="."' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.13/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.13/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.13/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.13/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="A"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="A"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="RR"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="RR"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="RA"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="RA"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="AR"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="AR"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="AA"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="AA"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="aA"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="aA"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="HET"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="HET"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.13/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.13/test/filter.7.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.13/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.13/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.13/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.13/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.13/bcftools sort -m 0 /builddir/build/BUILD/bcftools-1.13/test/sort.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.13/bcftools sort -Ob -m 0 /builddir/build/BUILD/bcftools-1.13/test/sort.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.13/bcftools sort -m 1000 /builddir/build/BUILD/bcftools-1.13/test/sort.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.13/bcftools sort -Ob -m 1000 /builddir/build/BUILD/bcftools-1.13/test/sort.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.13/test/regions.tab /tmp/MM8SwH8Pi0/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.13/test/regions.tab .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /builddir/build/BUILD/bcftools-1.13/test/regions.tab /tmp/MM8SwH8Pi0/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MM8SwH8Pi0/regions.tab.gz /tmp/MM8SwH8Pi0/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MM8SwH8Pi0/regions.tab.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/MM8SwH8Pi0/regions.tab.gz /tmp/MM8SwH8Pi0/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MM8SwH8Pi0/regions.bed /tmp/MM8SwH8Pi0/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MM8SwH8Pi0/regions.bed .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/MM8SwH8Pi0/regions.bed /tmp/MM8SwH8Pi0/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MM8SwH8Pi0/regions.bed.gz /tmp/MM8SwH8Pi0/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MM8SwH8Pi0/regions.bed.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/MM8SwH8Pi0/regions.bed.gz /tmp/MM8SwH8Pi0/regions.vcf.gz .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/MM8SwH8Pi0/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/MM8SwH8Pi0/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.13/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.13/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -x FORMAT /builddir/build/BUILD/bcftools-1.13/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -x FORMAT /builddir/build/BUILD/bcftools-1.13/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots4.vcf.gz -c +INFO /tmp/MM8SwH8Pi0/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots4.vcf.gz -c +INFO /tmp/MM8SwH8Pi0/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.13/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.13/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.13/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.13/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.13/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.13/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots11.vcf.gz -c FMT /tmp/MM8SwH8Pi0/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots11.vcf.gz -c FMT /tmp/MM8SwH8Pi0/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c FMT/newGT:=GT /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots2.vcf.gz -c FMT/newGT:=GT /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots12.vcf.gz -c FMT/GT:=newGT /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots12.vcf.gz -c FMT/GT:=newGT /tmp/MM8SwH8Pi0/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.13/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.13/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.13/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.13/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.13/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.13/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.13/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.13/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.13/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.13/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.13/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.13/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -x FILTER /builddir/build/BUILD/bcftools-1.13/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -x FILTER /builddir/build/BUILD/bcftools-1.13/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.13/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.13/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.13/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.13/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.13/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.13/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/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-1.13/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/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-1.13/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/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-1.13/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/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-1.13/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/MM8SwH8Pi0/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/MM8SwH8Pi0/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/MM8SwH8Pi0/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/MM8SwH8Pi0/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate20.src.vcf.gz -c FMT/GT /tmp/MM8SwH8Pi0/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate20.src.vcf.gz -c FMT/GT /tmp/MM8SwH8Pi0/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate20.src.vcf.gz -c +FMT/GT /tmp/MM8SwH8Pi0/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate20.src.vcf.gz -c +FMT/GT /tmp/MM8SwH8Pi0/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate20.src.vcf.gz -c -FMT/GT /tmp/MM8SwH8Pi0/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate20.src.vcf.gz -c -FMT/GT /tmp/MM8SwH8Pi0/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.13/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.13/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/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-1.13/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/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-1.13/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.13/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.13/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate --rename-annots /builddir/build/BUILD/bcftools-1.13/test/annotate21.txt /builddir/build/BUILD/bcftools-1.13/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob --rename-annots /builddir/build/BUILD/bcftools-1.13/test/annotate21.txt /builddir/build/BUILD/bcftools-1.13/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/MM8SwH8Pi0/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/MM8SwH8Pi0/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/MM8SwH8Pi0/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.13/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/MM8SwH8Pi0/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.13/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +missing2ref --no-version /tmp/MM8SwH8Pi0/plugin1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +missing2ref --no-version /tmp/MM8SwH8Pi0/plugin1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/plugin1.vcf.gz -- -t . -n 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/plugin1.bcf -- -t . -n 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/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-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.13/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.13/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.13/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.13/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.13/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.13/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.3.vcf.gz -- -t a -n pM | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.3.bcf -- -t a -n pM | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.3.vcf.gz -- -t a -n pm | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.3.bcf -- -t a -n pm | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.3.vcf.gz -- -t a -n c:1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.3.bcf -- -t a -n c:1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.3.vcf.gz -- -t a -n c:"1|1" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.3.bcf -- -t a -n c:"1|1" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.3.vcf.gz -- -t a -n c:"m|M" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.3.bcf -- -t a -n c:"m|M" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.3.vcf.gz -- -t a -n c:0/1/1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/MM8SwH8Pi0/setGT.3.bcf -- -t a -n c:0/1/1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-AN-AC --no-version /tmp/MM8SwH8Pi0/plugin1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-AN-AC --no-version /tmp/MM8SwH8Pi0/plugin1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +dosage /tmp/MM8SwH8Pi0/dosage.vcf.gz -- -t PL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +dosage /tmp/MM8SwH8Pi0/dosage.bcf -- -t PL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +dosage /tmp/MM8SwH8Pi0/dosage.vcf.gz -- -t GL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +dosage /tmp/MM8SwH8Pi0/dosage.bcf -- -t GL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +dosage /tmp/MM8SwH8Pi0/dosage.vcf.gz -- -t GT | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +dosage /tmp/MM8SwH8Pi0/dosage.bcf -- -t GT | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fixploidy --no-version /tmp/MM8SwH8Pi0/fixploidy.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.13/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.13/test/fixploidy.ploidy | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fixploidy --no-version /tmp/MM8SwH8Pi0/fixploidy.bcf -- -s /builddir/build/BUILD/bcftools-1.13/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.13/test/fixploidy.ploidy | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +guess-ploidy /tmp/MM8SwH8Pi0/view.PL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +guess-ploidy /tmp/MM8SwH8Pi0/view.PL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +guess-ploidy /tmp/MM8SwH8Pi0/view.GL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +guess-ploidy /tmp/MM8SwH8Pi0/view.GL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +tag2tag --no-version /tmp/MM8SwH8Pi0/view.GL.vcf.gz -- -r --gl-to-pl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +tag2tag --no-version /tmp/MM8SwH8Pi0/view.GL.bcf -- -r --gl-to-pl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +tag2tag --no-version /tmp/MM8SwH8Pi0/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +tag2tag --no-version /tmp/MM8SwH8Pi0/view.GP.bcf -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +add-variantkey /tmp/MM8SwH8Pi0/query.variantkey.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +add-variantkey /tmp/MM8SwH8Pi0/query.variantkey.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +variantkey-hex /tmp/MM8SwH8Pi0/query.variantkey.vcf.gz test/ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +variantkey-hex /tmp/MM8SwH8Pi0/query.variantkey.bcf test/ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +allele-length /tmp/MM8SwH8Pi0/query.nucleotide.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +allele-length /tmp/MM8SwH8Pi0/query.nucleotide.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/view.vcf.gz -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/view.bcf -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/view.vcf.gz -- -t AC -S /builddir/build/BUILD/bcftools-1.13/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/view.bcf -- -t AC -S /builddir/build/BUILD/bcftools-1.13/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/view.vcf.gz -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.13/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/view.bcf -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.13/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/many-alts.vcf.gz -- -t AN,AC | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/many-alts.bcf -- -t AN,AC | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-hemi.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-hemi.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-hemi.vcf.gz -- -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-hemi.bcf -- -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-hwe.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-hwe.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-hwe.vcf.gz -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-hwe.bcf -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-AN0.vcf.gz -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-AN0.bcf -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-VAF.vcf.gz -- -t VAF,VAF1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-VAF.bcf -- -t VAF,VAF1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-AD.vcf.gz -- -t 'DP:1=int(sum(AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/MM8SwH8Pi0/fill-tags-AD.bcf -- -t 'DP:1=int(sum(AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.vcf.gz | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.bcf | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.vcf.gz -- -H | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.bcf -- -H | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.vcf.gz -- -Hm | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.bcf -- -Hm | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.vcf.gz -- -Hmv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.bcf -- -Hmv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.vcf.gz -- -Hv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.bcf -- -Hv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.vcf.gz -- -m | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.bcf -- -m | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.vcf.gz -- -mv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.bcf -- -mv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.vcf.gz -- -v | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/MM8SwH8Pi0/view.bcf -- -v | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-switch-rate /tmp/MM8SwH8Pi0/trio.vcf.gz -- -p /builddir/build/BUILD/bcftools-1.13/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-switch-rate /tmp/MM8SwH8Pi0/trio.bcf -- -p /builddir/build/BUILD/bcftools-1.13/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-stats /tmp/MM8SwH8Pi0/trio-stats.vcf.gz -a 1 -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-stats /tmp/MM8SwH8Pi0/trio-stats.bcf -a 1 -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-stats /tmp/MM8SwH8Pi0/trio-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-stats /tmp/MM8SwH8Pi0/trio-stats.bcf -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +smpl-stats /tmp/MM8SwH8Pi0/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +smpl-stats /tmp/MM8SwH8Pi0/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +indel-stats /tmp/MM8SwH8Pi0/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +indel-stats /tmp/MM8SwH8Pi0/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +indel-stats /tmp/MM8SwH8Pi0/indel-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +indel-stats /tmp/MM8SwH8Pi0/indel-stats.bcf -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +indel-stats /tmp/MM8SwH8Pi0/indel-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +indel-stats /tmp/MM8SwH8Pi0/indel-stats.bcf -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/MM8SwH8Pi0/ad-bias.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/MM8SwH8Pi0/ad-bias.bcf -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/MM8SwH8Pi0/ad-bias.2.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/MM8SwH8Pi0/ad-bias.2.bcf -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/MM8SwH8Pi0/ad-bias.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/MM8SwH8Pi0/ad-bias.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/MM8SwH8Pi0/ad-bias.2.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/MM8SwH8Pi0/ad-bias.2.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +af-dist /tmp/MM8SwH8Pi0/af-dist.vcf.gz | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +af-dist /tmp/MM8SwH8Pi0/af-dist.bcf | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/MM8SwH8Pi0/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -i /tmp/MM8SwH8Pi0/fixref.2b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/MM8SwH8Pi0/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -i /tmp/MM8SwH8Pi0/fixref.2b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/MM8SwH8Pi0/fixref.3.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/fixref.3.fa -m top | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/MM8SwH8Pi0/fixref.3.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/fixref.3.fa -m top | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/MM8SwH8Pi0/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -m ref-alt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/MM8SwH8Pi0/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -m ref-alt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/MM8SwH8Pi0/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -m flip | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/MM8SwH8Pi0/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -m flip | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-from-fasta /tmp/MM8SwH8Pi0/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.13/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-from-fasta /tmp/MM8SwH8Pi0/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.13/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-from-fasta /tmp/MM8SwH8Pi0/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/aa.fa -c REF -N | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-from-fasta /tmp/MM8SwH8Pi0/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/aa.fa -c REF -N | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-from-fasta /tmp/MM8SwH8Pi0/ref.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -c REF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +fill-from-fasta /tmp/MM8SwH8Pi0/ref.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -c REF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTsubset --no-version /tmp/MM8SwH8Pi0/view.vcf.gz -- -s NA00001 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTsubset --no-version /tmp/MM8SwH8Pi0/view.bcf -- -s NA00001 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTsubset --no-version /tmp/MM8SwH8Pi0/view.vcf.gz -- -s NA00001,NA00002 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTsubset --no-version /tmp/MM8SwH8Pi0/view.bcf -- -s NA00001,NA00002 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTsubset --no-version /tmp/MM8SwH8Pi0/view.vcf.gz -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +GTsubset --no-version /tmp/MM8SwH8Pi0/view.bcf -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/MM8SwH8Pi0/mendelian.vcf.gz -t mom1,dad1,child1 -md | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/MM8SwH8Pi0/mendelian.bcf -t mom1,dad1,child1 -md | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/MM8SwH8Pi0/mendelian.vcf.gz -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/MM8SwH8Pi0/mendelian.bcf -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/MM8SwH8Pi0/mendelian.vcf.gz -t mom1,dad1,child1 -mx | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/MM8SwH8Pi0/mendelian.bcf -t mom1,dad1,child1 -mx | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/MM8SwH8Pi0/mendelian.vcf.gz -t mom1,dad1,child1 -ma | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/MM8SwH8Pi0/mendelian.bcf -t mom1,dad1,child1 -ma | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/MM8SwH8Pi0/mendelian.vcf.gz -t mom1,dad1,child1 -mu | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/MM8SwH8Pi0/mendelian.bcf -t mom1,dad1,child1 -mu | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/MM8SwH8Pi0/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/MM8SwH8Pi0/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/MM8SwH8Pi0/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.13/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.13/test/contrast1.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/MM8SwH8Pi0/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.13/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.13/test/contrast1.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/MM8SwH8Pi0/contrast.1.vcf.gz -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/MM8SwH8Pi0/contrast.1.bcf -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/MM8SwH8Pi0/contrast.1.vcf.gz -a NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/MM8SwH8Pi0/contrast.1.bcf -a NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.1.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.1.bcf -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.2.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.2.bcf -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.4.bcf -p proband,father,mother | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.8.vcf.gz -p proband,father,mother | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.8.bcf -p proband,father,mother | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.9.vcf.gz -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.9.bcf -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.9.vcf.gz -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/MM8SwH8Pi0/trio-dnm/trio-dnm.9.bcf -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +gvcfz /tmp/MM8SwH8Pi0/gvcfz.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools +gvcfz /tmp/MM8SwH8Pi0/gvcfz.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools +gvcfz /tmp/MM8SwH8Pi0/gvcfz.vcf.gz -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools +gvcfz /tmp/MM8SwH8Pi0/gvcfz.bcf -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools +gvcfz /tmp/MM8SwH8Pi0/gvcfz.2.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools +gvcfz /tmp/MM8SwH8Pi0/gvcfz.2.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools +remove-overlaps /tmp/MM8SwH8Pi0/remove-overlaps.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +remove-overlaps /tmp/MM8SwH8Pi0/remove-overlaps.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +remove-overlaps /tmp/MM8SwH8Pi0/remove-overlaps.vcf.gz -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +remove-overlaps /tmp/MM8SwH8Pi0/remove-overlaps.bcf -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.vcf.gz -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.bcf -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.vcf.gz -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.bcf -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.vcf.gz -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.bcf -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.2.vcf.gz -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.2.bcf -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.2.vcf.gz -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.2.bcf -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.3.vcf.gz -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.3.bcf -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.vcf.gz -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.bcf -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.vcf.gz -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.bcf -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.5.vcf.gz -s :synonymous -c Consequence | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.5.bcf -s :synonymous -c Consequence | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.5.vcf.gz -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.5.bcf -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.6.vcf.gz -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.6.bcf -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.6.vcf.gz -c - | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.6.bcf -c - | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.6.vcf.gz -c - -s worst | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/split-vep.6.bcf -c - -s worst | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +split-vep /tmp/MM8SwH8Pi0/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-1.13/bcftools +parental-origin /tmp/MM8SwH8Pi0/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-1.13/bcftools +parental-origin /tmp/MM8SwH8Pi0/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-1.13/bcftools +parental-origin /tmp/MM8SwH8Pi0/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-1.13/bcftools +parental-origin /tmp/MM8SwH8Pi0/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-1.13/bcftools +parental-origin /tmp/MM8SwH8Pi0/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-1.13/bcftools +parental-origin /tmp/MM8SwH8Pi0/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-1.13/bcftools +parental-origin /tmp/MM8SwH8Pi0/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-1.13/bcftools +parental-origin /tmp/MM8SwH8Pi0/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-1.13/bcftools +parental-origin /tmp/MM8SwH8Pi0/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-1.13/bcftools +parental-origin /tmp/MM8SwH8Pi0/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-1.13/bcftools +prune -w 1 -a r2,LD,HD /tmp/MM8SwH8Pi0/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 1 -a r2,LD,HD /tmp/MM8SwH8Pi0/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 1 -a r2,LD,HD /tmp/MM8SwH8Pi0/prune.2.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 1 -a r2,LD,HD /tmp/MM8SwH8Pi0/prune.2.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/MM8SwH8Pi0/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/MM8SwH8Pi0/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/MM8SwH8Pi0/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/MM8SwH8Pi0/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/MM8SwH8Pi0/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/MM8SwH8Pi0/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/MM8SwH8Pi0/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/MM8SwH8Pi0/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 -N 1st /tmp/MM8SwH8Pi0/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 -N 1st /tmp/MM8SwH8Pi0/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/MM8SwH8Pi0/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/MM8SwH8Pi0/prune.1.bcf | grep -v ^##bcftools_ .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/MM8SwH8Pi0/split.1.1 && cd /tmp/MM8SwH8Pi0/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-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/MM8SwH8Pi0/split.1.2 -S /builddir/build/BUILD/bcftools-1.13/test/split.smpl.1.2.txt && cd /tmp/MM8SwH8Pi0/split.1.2 && for f in A.vcf B.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/MM8SwH8Pi0/split.1.3 -S /builddir/build/BUILD/bcftools-1.13/test/split.smpl.1.3.txt && cd /tmp/MM8SwH8Pi0/split.1.3 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/MM8SwH8Pi0/split.1.4 -S /builddir/build/BUILD/bcftools-1.13/test/split.smpl.1.3.txt -i 'GT[0]="alt"' && cd /tmp/MM8SwH8Pi0/split.1.4 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/MM8SwH8Pi0/split.1.5 -S /builddir/build/BUILD/bcftools-1.13/test/split.smpl.1.3.txt -i 'GT="alt"' && cd /tmp/MM8SwH8Pi0/split.1.5 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/MM8SwH8Pi0/split.1.6 -S /builddir/build/BUILD/bcftools-1.13/test/split.smpl.1.4.txt -i 'GT="alt"' && cd /tmp/MM8SwH8Pi0/split.1.6 && for f in file1.vcf file2.vcf file3.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/MM8SwH8Pi0/split.1.7 -G /builddir/build/BUILD/bcftools-1.13/test/split.grp.1.1.txt && cd /tmp/MM8SwH8Pi0/split.1.7 && for f in A.vcf A1.vcf A2.vcf B.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.2.vcf -o /tmp/MM8SwH8Pi0/split.2.1 && cd /tmp/MM8SwH8Pi0/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-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.13/bcftools +scatter /builddir/build/BUILD/bcftools-1.13/test/scatter.1.vcf -o /tmp/MM8SwH8Pi0/scatter.1.1 -n 3 && cd /tmp/MM8SwH8Pi0/scatter.1.1 && cat 0.vcf 1.vcf 2.vcf | grep -v ^## .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.13/bcftools +scatter /builddir/build/BUILD/bcftools-1.13/test/scatter.1.vcf -o /tmp/MM8SwH8Pi0/scatter.1.2 -s 21,22 && cd /tmp/MM8SwH8Pi0/scatter.1.2 && cat 21.vcf 22.vcf | grep -v ^## .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.13/bcftools +scatter /builddir/build/BUILD/bcftools-1.13/test/scatter.1.vcf -o /tmp/MM8SwH8Pi0/scatter.1.3 -s 21,22 -x X && cd /tmp/MM8SwH8Pi0/scatter.1.3 && cat 21.vcf 22.vcf X.vcf | grep -v ^## .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version /tmp/MM8SwH8Pi0/concat.1.a.vcf.gz /tmp/MM8SwH8Pi0/concat.1.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob /tmp/MM8SwH8Pi0/concat.1.a.vcf.gz /tmp/MM8SwH8Pi0/concat.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version /tmp/MM8SwH8Pi0/concat.1.a.bcf /tmp/MM8SwH8Pi0/concat.1.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob /tmp/MM8SwH8Pi0/concat.1.a.bcf /tmp/MM8SwH8Pi0/concat.1.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -a /tmp/MM8SwH8Pi0/concat.2.a.vcf.gz /tmp/MM8SwH8Pi0/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -a /tmp/MM8SwH8Pi0/concat.2.a.vcf.gz /tmp/MM8SwH8Pi0/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -a /tmp/MM8SwH8Pi0/concat.2.a.bcf /tmp/MM8SwH8Pi0/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -a /tmp/MM8SwH8Pi0/concat.2.a.bcf /tmp/MM8SwH8Pi0/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -aD /tmp/MM8SwH8Pi0/concat.2.a.vcf.gz /tmp/MM8SwH8Pi0/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -aD /tmp/MM8SwH8Pi0/concat.2.a.vcf.gz /tmp/MM8SwH8Pi0/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -aD /tmp/MM8SwH8Pi0/concat.2.a.bcf /tmp/MM8SwH8Pi0/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -aD /tmp/MM8SwH8Pi0/concat.2.a.bcf /tmp/MM8SwH8Pi0/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -l /tmp/MM8SwH8Pi0/concat.3.a.vcf.gz /tmp/MM8SwH8Pi0/concat.3.b.vcf.gz /tmp/MM8SwH8Pi0/concat.3.0.vcf.gz /tmp/MM8SwH8Pi0/concat.3.c.vcf.gz /tmp/MM8SwH8Pi0/concat.3.d.vcf.gz /tmp/MM8SwH8Pi0/concat.3.e.vcf.gz /tmp/MM8SwH8Pi0/concat.3.f.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -l /tmp/MM8SwH8Pi0/concat.3.a.vcf.gz /tmp/MM8SwH8Pi0/concat.3.b.vcf.gz /tmp/MM8SwH8Pi0/concat.3.0.vcf.gz /tmp/MM8SwH8Pi0/concat.3.c.vcf.gz /tmp/MM8SwH8Pi0/concat.3.d.vcf.gz /tmp/MM8SwH8Pi0/concat.3.e.vcf.gz /tmp/MM8SwH8Pi0/concat.3.f.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -l /tmp/MM8SwH8Pi0/concat.3.a.bcf /tmp/MM8SwH8Pi0/concat.3.b.bcf /tmp/MM8SwH8Pi0/concat.3.0.bcf /tmp/MM8SwH8Pi0/concat.3.c.bcf /tmp/MM8SwH8Pi0/concat.3.d.bcf /tmp/MM8SwH8Pi0/concat.3.e.bcf /tmp/MM8SwH8Pi0/concat.3.f.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -l /tmp/MM8SwH8Pi0/concat.3.a.bcf /tmp/MM8SwH8Pi0/concat.3.b.bcf /tmp/MM8SwH8Pi0/concat.3.0.bcf /tmp/MM8SwH8Pi0/concat.3.c.bcf /tmp/MM8SwH8Pi0/concat.3.d.bcf /tmp/MM8SwH8Pi0/concat.3.e.bcf /tmp/MM8SwH8Pi0/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1878132763 .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat --naive-force /tmp/MM8SwH8Pi0/naive_concat.0.bcf /tmp/MM8SwH8Pi0/naive_concat.1.bcf /tmp/MM8SwH8Pi0/naive_concat.2.bcf /tmp/MM8SwH8Pi0/naive_concat.3.bcf /tmp/MM8SwH8Pi0/naive_concat.4.bcf /tmp/MM8SwH8Pi0/naive_concat.5.bcf /tmp/MM8SwH8Pi0/naive_concat.6.bcf /tmp/MM8SwH8Pi0/naive_concat.7.bcf /tmp/MM8SwH8Pi0/naive_concat.8.bcf /tmp/MM8SwH8Pi0/naive_concat.9.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view -H .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat --naive /tmp/MM8SwH8Pi0/naive_concat.0.vcf.gz /tmp/MM8SwH8Pi0/naive_concat.1.vcf.gz /tmp/MM8SwH8Pi0/naive_concat.2.vcf.gz /tmp/MM8SwH8Pi0/naive_concat.3.vcf.gz /tmp/MM8SwH8Pi0/naive_concat.4.vcf.gz /tmp/MM8SwH8Pi0/naive_concat.5.vcf.gz /tmp/MM8SwH8Pi0/naive_concat.6.vcf.gz /tmp/MM8SwH8Pi0/naive_concat.7.vcf.gz /tmp/MM8SwH8Pi0/naive_concat.8.vcf.gz /tmp/MM8SwH8Pi0/naive_concat.9.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view -H .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -l /tmp/MM8SwH8Pi0/concat.4.a.vcf.gz /tmp/MM8SwH8Pi0/concat.4.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -l /tmp/MM8SwH8Pi0/concat.4.a.vcf.gz /tmp/MM8SwH8Pi0/concat.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -l /tmp/MM8SwH8Pi0/concat.4.a.bcf /tmp/MM8SwH8Pi0/concat.4.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -l /tmp/MM8SwH8Pi0/concat.4.a.bcf /tmp/MM8SwH8Pi0/concat.4.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.hdr /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.hdr /tmp/MM8SwH8Pi0/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MM8SwH8Pi0/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.hdr /tmp/MM8SwH8Pi0/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MM8SwH8Pi0/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples /tmp/MM8SwH8Pi0/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MM8SwH8Pi0/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples /tmp/MM8SwH8Pi0/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MM8SwH8Pi0/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples2 /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples2 /tmp/MM8SwH8Pi0/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MM8SwH8Pi0/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples2 /tmp/MM8SwH8Pi0/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MM8SwH8Pi0/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples3 /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples3 /tmp/MM8SwH8Pi0/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MM8SwH8Pi0/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples3 /tmp/MM8SwH8Pi0/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MM8SwH8Pi0/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples4 /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples4 /tmp/MM8SwH8Pi0/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MM8SwH8Pi0/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples4 /tmp/MM8SwH8Pi0/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MM8SwH8Pi0/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.empty.hdr /builddir/build/BUILD/bcftools-1.13/test/empty.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.13/test/empty.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.empty.hdr /tmp/MM8SwH8Pi0/empty.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MM8SwH8Pi0/empty.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.empty.hdr /tmp/MM8SwH8Pi0/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MM8SwH8Pi0/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -f /builddir/build/BUILD/bcftools-1.13/test/reheader.fai /builddir/build/BUILD/bcftools-1.13/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -f /builddir/build/BUILD/bcftools-1.13/test/reheader.fai /tmp/MM8SwH8Pi0/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -f /builddir/build/BUILD/bcftools-1.13/test/reheader.fai /tmp/MM8SwH8Pi0/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.13/test/reheader.fai /builddir/build/BUILD/bcftools-1.13/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.13/test/reheader.fai /tmp/MM8SwH8Pi0/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.13/test/reheader.fai /tmp/MM8SwH8Pi0/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.13/bcftools annotate --rename-chrs /tmp/MM8SwH8Pi0/rename.map -Ov /tmp/MM8SwH8Pi0/annotate.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.13/bcftools annotate --rename-chrs /tmp/MM8SwH8Pi0/rename.map -Ob /tmp/MM8SwH8Pi0/annotate.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.13/bcftools annotate --rename-chrs /tmp/MM8SwH8Pi0/rename.map -Ov /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.13/bcftools annotate --rename-chrs /tmp/MM8SwH8Pi0/rename.map -Ob /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. /tmp/MM8SwH8Pi0/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- /tmp/MM8SwH8Pi0/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --tag PL /tmp/MM8SwH8Pi0/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --tag PL /tmp/MM8SwH8Pi0/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --vcf-ids /tmp/MM8SwH8Pi0/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --vcf-ids /tmp/MM8SwH8Pi0/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --chrom /tmp/MM8SwH8Pi0/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --chrom .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --chrom /tmp/MM8SwH8Pi0/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --chrom .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --chrom --vcf-ids /tmp/MM8SwH8Pi0/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --chrom --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --chrom --vcf-ids /tmp/MM8SwH8Pi0/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --chrom --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert -h -,.,. /tmp/MM8SwH8Pi0/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -h -,.,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert -h .,-,. /tmp/MM8SwH8Pi0/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -h .,-,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert -h .,.,- /tmp/MM8SwH8Pi0/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.13/bcftools convert -H /builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.13/bcftools convert -H /builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^## .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.13/bcftools convert --vcf-ids -H /builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.13/bcftools convert --vcf-ids -H /builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.13/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.13/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.13/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.13/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^## .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert --hapsample -,. /tmp/MM8SwH8Pi0/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert --hapsample -,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert --hapsample .,- /tmp/MM8SwH8Pi0/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert --hapsample .,- .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools convert --haplegendsample -,.,. /tmp/MM8SwH8Pi0/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/convert.hap-missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.13/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/MM8SwH8Pi0/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/MM8SwH8Pi0/convert.gvcf.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.13/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.13/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.13/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.13/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.13/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.13/test/convert.23andme | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab -c /tmp/MM8SwH8Pi0/consensus.1.chain.new >/dev/null; cat /tmp/MM8SwH8Pi0/consensus.1.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab -c /tmp/MM8SwH8Pi0/consensus.2.chain.new >/dev/null; cat /tmp/MM8SwH8Pi0/consensus.2.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab --mask-with X -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab -c /tmp/MM8SwH8Pi0/consensus.3.chain.new >/dev/null; cat /tmp/MM8SwH8Pi0/consensus.3.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -H 1 -c /tmp/MM8SwH8Pi0/consensus.4.chain.new >/dev/null; cat /tmp/MM8SwH8Pi0/consensus.4.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/empty.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus4.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus2.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus5.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus6.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus6.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -a . .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -a . -i 'ALT!=""' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -a . -e 'MinDP>15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -a . -e 'MinDP<15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.12.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.13.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.13.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.14.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.14.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.12.fa --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.15.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -I .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/MM8SwH8Pi0/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -H I .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -b /tmp/MM8SwH8Pi0/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob -b /tmp/MM8SwH8Pi0/mpileup.bam.urllist | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -b /tmp/MM8SwH8Pi0/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob -b /tmp/MM8SwH8Pi0/mpileup.cram.urllist | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/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-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/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-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/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-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/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-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.13/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.13/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.13/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.13/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq.gff3 /builddir/build/BUILD/bcftools-1.13/test/csq.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq.chr.gff3 /builddir/build/BUILD/bcftools-1.13/test/csq.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq.2.gff /builddir/build/BUILD/bcftools-1.13/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq.2.gff --ncsq 64 /builddir/build/BUILD/bcftools-1.13/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000256452/ENST00000256452.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000256452/ENST00000256452.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000256452/intron.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENSG00000173376/ENSG00000173376.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENSG00000173376/ENSG00000173376.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENSG00000173376/synon.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/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-1.13/test/csq/ENSMUST00000133836 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000381157/ENST00000381157.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000381157/ENST00000381157.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000381157/haploid-diploid.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000357367/ENST00000357367.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000357367/ENST00000357367.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000357367/stop-retained.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000545279/ENST00000545279.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000545279/ENST00000545279.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000545279/splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000519442/ENST00000519442.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000519442/ENST00000519442.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000519442/synon-splice-region-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000301246/ENST00000301246.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000301246/ENST00000301246.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000301246/15bp-insert.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000448695/ENST00000448695.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000448695/ENST00000448695.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000368801/ENST00000368801.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000368801/ENST00000368801.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000368801/compound-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000227471/ENST00000227471.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000227471/ENST00000227471.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249.2/ENST00000318249.2.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000375992/ENST00000375992.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000375992/ENST00000375992.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000624631/ENST00000624631.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000624631/ENST00000624631.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000624631/ambiguous.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420190/ENST00000420190.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420190/ENST00000420190.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420190/abort-in-csq-push.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520868/ENST00000520868.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520868/ENST00000520868.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520868/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/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-1.13/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.13/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.13/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000400151/ENST00000400151.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000400151/ENST00000400151.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000400151/long-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000518414/ENST00000518414.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000518414/ENST00000518414.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000436063/ENST00000436063.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000436063/ENST00000436063.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000436063/insert-before-utr.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000410009/ENST00000410009.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000410009/ENST00000410009.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000410009/frameshift.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/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-1.13/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000271583/ENST00000271583.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000271583/ENST00000271583.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000271583/splice-acceptor.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000409523/ENST00000409523.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000409523/ENST00000409523.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000409523/long-overlapping-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000263103-INS/insertions.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/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-1.13/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/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-1.13/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000390520/ENST00000390520.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000390520/ENST00000390520.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000390520/deletion-overlap.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000557788/ENST00000557788.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000557788/ENST00000557788.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000557788/long-overlap-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000413103/ENST00000413103.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000413103/ENST00000413103.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000413103/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000368801.2/ENST00000368801.2.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000368801.2/start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/start-lost-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000593942/ENST00000593942.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000593942/ENST00000593942.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000593942/last-codon-deletion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000382647/ENST00000382647.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000382647/ENST00000382647.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0002/EDUMMY0002.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0002/EDUMMY0002.gff /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0002/boundaries.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420670/start-stop-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420670/segfault.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0003/EDUMMY0003.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0003/EDUMMY0003.gff /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0003/long-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000528237/ENST00000528237.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000528237/ENST00000528237.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000230048/ENST00000230048.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000230048/ENST00000230048.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000230048/start-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.13/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.13/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/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-1.13/bcftools gtcheck -e 0 /tmp/MM8SwH8Pi0/gtcheck.1.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u GT,GT /tmp/MM8SwH8Pi0/gtcheck.1.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u GT,PL /tmp/MM8SwH8Pi0/gtcheck.1.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u PL,GT /tmp/MM8SwH8Pi0/gtcheck.1.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u PL,PL /tmp/MM8SwH8Pi0/gtcheck.1.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -p s1,s1 /tmp/MM8SwH8Pi0/gtcheck.1.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 /tmp/MM8SwH8Pi0/gtcheck.2.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 /tmp/MM8SwH8Pi0/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/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/MM8SwH8Pi0/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.13/test/gtcheck.3.pairs /tmp/MM8SwH8Pi0/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u PL /tmp/MM8SwH8Pi0/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 --n-matches 4 /tmp/MM8SwH8Pi0/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/MM8SwH8Pi0/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/MM8SwH8Pi0/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/MM8SwH8Pi0/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/MM8SwH8Pi0/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/MM8SwH8Pi0/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -p B,C,B,D /tmp/MM8SwH8Pi0/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u GT,GT -H /tmp/MM8SwH8Pi0/gtcheck.1.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u GT,PL -H /tmp/MM8SwH8Pi0/gtcheck.1.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u PL,GT -H /tmp/MM8SwH8Pi0/gtcheck.1.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u PL,PL -H /tmp/MM8SwH8Pi0/gtcheck.1.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.13/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/MM8SwH8Pi0/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.13/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/MM8SwH8Pi0/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -u GT -e 30 /tmp/MM8SwH8Pi0/gtcheck.1.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/MM8SwH8Pi0/gtcheck.1.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -u GT -e 300 /tmp/MM8SwH8Pi0/gtcheck.1.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -u PL -e 30 /tmp/MM8SwH8Pi0/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck /tmp/MM8SwH8Pi0/gtcheck.ntop.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck --n-matches 2 /tmp/MM8SwH8Pi0/gtcheck.ntop.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.13/bcftools gtcheck /tmp/MM8SwH8Pi0/gtcheck.5.vcf.gz -g /tmp/MM8SwH8Pi0/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok Number of tests: total .. 1542 passed .. 1542 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: bcftools-1.13-1.fc35.i686 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.t217l8 + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.13 + DOCDIR=/builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/share/doc/bcftools + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/share/doc/bcftools + cp -pr AUTHORS /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/share/doc/bcftools + cp -pr NEWS /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/share/doc/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.stVfIr + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.13 + LICENSEDIR=/builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/share/licenses/bcftools + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/share/licenses/bcftools + cp -pr LICENSE /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386/usr/share/licenses/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Provides: bcftools = 1.13-1.fc35 bcftools(x86-32) = 1.13-1.fc35 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 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.33) libc.so.6(GLIBC_2.34) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libgsl.so.25 libgslcblas.so.0 libhts.so.3 libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libm.so.6(GLIBC_2.23) libm.so.6(GLIBC_2.29) libperl.so.5.34 libz.so.1 rtld(GNU_HASH) Conflicts: samtools < 1.0 Processing files: bcftools-debugsource-1.13-1.fc35.i686 Provides: bcftools-debugsource = 1.13-1.fc35 bcftools-debugsource(x86-32) = 1.13-1.fc35 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bcftools-debuginfo-1.13-1.fc35.i686 Provides: bcftools-debuginfo = 1.13-1.fc35 bcftools-debuginfo(x86-32) = 1.13-1.fc35 debuginfo(build-id) = 07036564b7f9faa694022f5746344f597b1ac323 debuginfo(build-id) = 1339f132bbaa2a5bfbd79f09e55dda3084c3d15c debuginfo(build-id) = 1a661e9ac2d544a71a7a9a1a5ce82efcf17220b0 debuginfo(build-id) = 237cb1327338a14f3f390151de5b4cbd7db766fe debuginfo(build-id) = 27d9dbb59939873e711d9c951e51502a178ad432 debuginfo(build-id) = 2b619efada30640171e5c1bd4a81b5ad638e2877 debuginfo(build-id) = 2df5c4945ac33d6bac3a44e6e0517ce83f858027 debuginfo(build-id) = 2e6dca74a8ba8653644ce6643c55742a56b1ef2c debuginfo(build-id) = 2eb202245d796a570ea6d32b58d359b2b03da7d1 debuginfo(build-id) = 30b1ce0af5f537ee93b4b936f2a089b0524c6506 debuginfo(build-id) = 3120564d29712b1f96503c87978e1e963b6d4161 debuginfo(build-id) = 3892b3174a4093ec5de9ef2d1f88563730759a0a debuginfo(build-id) = 3c4ffb40f9ff0226d860d4c1f39d6ed946f0e5fe debuginfo(build-id) = 3e3a52c0c1a89f6458a0bd83a2ae99d0080b4173 debuginfo(build-id) = 4e36d7caa4e959934b0dc3a9c81c5d36ac8e4c12 debuginfo(build-id) = 525af2e01988d66e856b9107ea694fa2d10eb128 debuginfo(build-id) = 549991d4e4f4ac71647050e3d71ca0d38cfdcfc3 debuginfo(build-id) = 57070038d2132a44fc7ab0494e4ce42bb3339a91 debuginfo(build-id) = 5cb390e3f9f815ebc624defc21009586f9b000a1 debuginfo(build-id) = 5cd9e0f90c2932ba6bcad3560eb37eaadaa060f1 debuginfo(build-id) = 633173356682e5be4192beea27a2159b4f8b7e6e debuginfo(build-id) = 67100980214dd44b49d870b9b6e6c29f3ed2b932 debuginfo(build-id) = 6ecde27f7fbed536605056a20e9ec2b7fe2280e0 debuginfo(build-id) = 72132cf20133cf429d0ffc9d7f7010fd76c4f341 debuginfo(build-id) = 7d896d34615771363dc7dbb71059fbd193f6af37 debuginfo(build-id) = 82232c911c6506fcba6b6040d708b268e0c527f9 debuginfo(build-id) = 8477c0aac25b9ed46176c7325b04c49ad4b6fc3f debuginfo(build-id) = 890ab2cd7150ea6542224ba4a7a87b8ab3cd1e13 debuginfo(build-id) = 8e72c837ab0a01c2adac2b277fdb86ff7d426ee8 debuginfo(build-id) = 94ed5623a7cfea844e70b1f5700f6271a232ee54 debuginfo(build-id) = 9c3693e40fd51934b78556724bca7ceff5cbe0bf debuginfo(build-id) = a875889373ea99ecf5936b8aea739da42ea9fd0f debuginfo(build-id) = c90560b4ad2f46da5b292a5bf458d2bf4d946cd9 debuginfo(build-id) = d0de1592b88fce3553e3d4af965be10b3d56d718 debuginfo(build-id) = de0082a27bbd3f39f2f4e498c30517c4afc8698c debuginfo(build-id) = e81820aeb68c70fef38368b68970fdd35c48f2d4 debuginfo(build-id) = ec3b413eb0192d23253e92541f45d3c68d9916eb debuginfo(build-id) = edca9d7d6a8ce52d5af173922083d4609c52b7e3 debuginfo(build-id) = fe6471d739a44e7da03764c88a2d054cd0e381ef Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bcftools-debugsource(x86-32) = 1.13-1.fc35 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386 Wrote: /builddir/build/RPMS/bcftools-debugsource-1.13-1.fc35.i686.rpm Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.13-1.fc35.i686.rpm Wrote: /builddir/build/RPMS/bcftools-1.13-1.fc35.i686.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.DPNY7z + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.13 + /usr/bin/rm -rf /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.i386 + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild bcftools-1.13-1.fc35.src.rpm Finish: build phase for bcftools-1.13-1.fc35.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-i686-1628447957.888446/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-i686-1628447957.888446/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-i686-1628447957.888446/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/bcftools-1.13-1.fc35.src.rpm) Config(child) 1 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 RPMResults tool