Warning: Permanently added '3.94.208.170' (ED25519) to the list of known hosts. Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-fkz6_ucv/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-fkz6_ucv/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1737371804.483416 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.0 starting (python version = 3.13.0, NVR = mock-6.0-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-fkz6_ucv/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-fkz6_ucv/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1737371804.483416 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-fkz6_ucv/bcftools/bcftools.spec) Config(fedora-41-i686) Start: clean chroot Finish: clean chroot Mock Version: 6.0 INFO: Mock Version: 6.0 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-41-i686-bootstrap-1737371804.483416/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using container image: registry.fedoraproject.org/fedora:41 INFO: Pulling image: registry.fedoraproject.org/fedora:41 INFO: Tagging container image as mock-bootstrap-2e604369-fff8-4c72-92fb-9ddac90898ad INFO: Checking that a432b057a522737c229d2aac9b029f55bf2a44eb3f423e4e4ece2acb8a304652 image matches host's architecture INFO: Copy content of container a432b057a522737c229d2aac9b029f55bf2a44eb3f423e4e4ece2acb8a304652 to /var/lib/mock/fedora-41-i686-bootstrap-1737371804.483416/root INFO: mounting a432b057a522737c229d2aac9b029f55bf2a44eb3f423e4e4ece2acb8a304652 with podman image mount INFO: image a432b057a522737c229d2aac9b029f55bf2a44eb3f423e4e4ece2acb8a304652 as /var/lib/containers/storage/overlay/c9636add90844f42998958a532f08e880f2904e56e7e03e6d453e29ae1b586c4/merged INFO: umounting image a432b057a522737c229d2aac9b029f55bf2a44eb3f423e4e4ece2acb8a304652 (/var/lib/containers/storage/overlay/c9636add90844f42998958a532f08e880f2904e56e7e03e6d453e29ae1b586c4/merged) with podman image umount INFO: Removing image mock-bootstrap-2e604369-fff8-4c72-92fb-9ddac90898ad INFO: Package manager dnf5 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-41-i686-1737371804.483416/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.20.0-1.fc41.x86_64 rpm-sequoia-1.7.0-3.fc41.x86_64 dnf5-5.2.8.1-3.fc41.x86_64 dnf5-plugins-5.2.8.1-3.fc41.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: local 100% | 174.8 KiB/s | 3.5 KiB | 00m00s Copr repository 100% | 89.6 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 644.5 KiB/s | 41.2 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash i686 5.2.32-1.fc41 local 8.3 MiB bzip2 i686 1.0.8-19.fc41 local 93.9 KiB coreutils i686 9.5-11.fc41 local 5.6 MiB cpio i686 2.15-2.fc41 local 1.1 MiB diffutils i686 3.10-8.fc41 local 1.6 MiB fedora-release noarch 41-29 local 0.0 B findutils i686 1:4.10.0-4.fc41 local 1.9 MiB gawk i686 5.3.0-4.fc41 local 1.7 MiB glibc-minimal-langpack i686 2.40-17.fc41 local 0.0 B grep i686 3.11-9.fc41 local 1.0 MiB gzip i686 1.13-2.fc41 local 388.1 KiB info i686 7.1-3.fc41 local 360.4 KiB patch i686 2.7.6-25.fc41 local 298.0 KiB redhat-rpm-config noarch 293-1.fc41 local 183.5 KiB rpm-build i686 4.20.0-1.fc41 local 178.2 KiB sed i686 4.9-3.fc41 local 860.6 KiB shadow-utils i686 2:4.15.1-12.fc41 local 4.0 MiB tar i686 2:1.35-4.fc41 local 3.0 MiB unzip i686 6.0-64.fc41 local 396.3 KiB util-linux i686 2.40.4-1.fc41 local 3.5 MiB which i686 2.21-42.fc41 local 78.9 KiB xz i686 1:5.6.2-2.fc41 local 1.2 MiB Installing dependencies: add-determinism i686 0.3.6-3.fc41 local 2.2 MiB alternatives i686 1.31-1.fc41 local 64.0 KiB ansible-srpm-macros noarch 1-16.fc41 local 35.7 KiB audit-libs i686 4.0.3-1.fc41 local 357.8 KiB authselect i686 1.5.0-8.fc41 local 160.6 KiB authselect-libs i686 1.5.0-8.fc41 local 825.4 KiB basesystem noarch 11-21.fc41 local 0.0 B binutils i686 2.43.1-5.fc41 local 25.3 MiB build-reproducibility-srpm-macros noarch 0.3.6-3.fc41 local 735.0 B bzip2-libs i686 1.0.8-19.fc41 local 76.0 KiB ca-certificates noarch 2024.2.69_v8.0.401-1.0.fc41 local 2.4 MiB coreutils-common i686 9.5-11.fc41 local 11.2 MiB cracklib i686 2.9.11-6.fc41 local 235.8 KiB crypto-policies noarch 20241029-1.git8baf557.fc41 local 136.9 KiB curl i686 8.9.1-3.fc41 local 796.6 KiB cyrus-sasl-lib i686 2.1.28-27.fc41 local 2.5 MiB debugedit i686 5.1-4.fc41 local 203.3 KiB dwz i686 0.15-8.fc41 local 328.9 KiB ed i686 1.20.2-2.fc41 local 141.7 KiB efi-srpm-macros noarch 5-13.fc41 local 40.2 KiB elfutils i686 0.192-7.fc41 local 2.6 MiB elfutils-debuginfod-client i686 0.192-7.fc41 local 79.8 KiB elfutils-default-yama-scope noarch 0.192-7.fc41 local 1.8 KiB elfutils-libelf i686 0.192-7.fc41 local 1.2 MiB elfutils-libs i686 0.192-7.fc41 local 704.9 KiB fedora-gpg-keys noarch 41-1 local 126.4 KiB fedora-release-common noarch 41-29 local 19.7 KiB fedora-release-identity-basic noarch 41-29 local 682.0 B fedora-repos noarch 41-1 local 4.9 KiB file i686 5.45-7.fc41 local 94.5 KiB file-libs i686 5.45-7.fc41 local 9.9 MiB filesystem i686 3.18-23.fc41 local 88.0 B fonts-srpm-macros noarch 1:2.0.5-17.fc41 local 55.8 KiB forge-srpm-macros noarch 0.4.0-1.fc41 local 38.9 KiB fpc-srpm-macros noarch 1.3-13.fc41 local 144.0 B gdb-minimal i686 15.2-4.fc41 local 13.3 MiB gdbm i686 1:1.23-7.fc41 local 449.8 KiB gdbm-libs i686 1:1.23-7.fc41 local 124.6 KiB ghc-srpm-macros noarch 1.9.1-2.fc41 local 747.0 B glibc i686 2.40-17.fc41 local 5.4 MiB glibc-common i686 2.40-17.fc41 local 1.0 MiB glibc-gconv-extra i686 2.40-17.fc41 local 7.5 MiB gmp i686 1:6.3.0-2.fc41 local 738.5 KiB gnat-srpm-macros noarch 6-6.fc41 local 1.0 KiB go-srpm-macros noarch 3.6.0-5.fc41 local 60.8 KiB jansson i686 2.13.1-10.fc41 local 87.6 KiB json-c i686 0.17-4.fc41 local 89.6 KiB kernel-srpm-macros noarch 1.0-24.fc41 local 1.9 KiB keyutils-libs i686 1.6.3-4.fc41 local 57.6 KiB krb5-libs i686 1.21.3-3.fc41 local 2.3 MiB libacl i686 2.3.2-2.fc41 local 39.3 KiB libarchive i686 3.7.4-4.fc41 local 994.3 KiB libattr i686 2.5.2-4.fc41 local 23.8 KiB libblkid i686 2.40.4-1.fc41 local 280.0 KiB libbrotli i686 1.1.0-5.fc41 local 859.5 KiB libcap i686 2.70-4.fc41 local 205.1 KiB libcap-ng i686 0.8.5-3.fc41 local 67.7 KiB libcom_err i686 1.47.1-6.fc41 local 62.4 KiB libcurl i686 8.9.1-3.fc41 local 836.9 KiB libeconf i686 0.6.2-3.fc41 local 61.2 KiB libevent i686 2.1.12-14.fc41 local 952.1 KiB libfdisk i686 2.40.4-1.fc41 local 403.6 KiB libffi i686 3.4.6-3.fc41 local 81.5 KiB libgcc i686 14.2.1-7.fc41 local 298.1 KiB libgomp i686 14.2.1-7.fc41 local 513.1 KiB libidn2 i686 2.3.7-2.fc41 local 324.3 KiB libmount i686 2.40.4-1.fc41 local 379.8 KiB libnghttp2 i686 1.62.1-2.fc41 local 173.5 KiB libnsl2 i686 2.0.1-2.fc41 local 57.2 KiB libpkgconf i686 2.3.0-1.fc41 local 80.7 KiB libpsl i686 0.21.5-4.fc41 local 75.8 KiB libpwquality i686 1.4.5-11.fc41 local 410.6 KiB libselinux i686 3.7-5.fc41 local 192.3 KiB libsemanage i686 3.7-2.fc41 local 304.1 KiB libsepol i686 3.7-2.fc41 local 873.4 KiB libsmartcols i686 2.40.4-1.fc41 local 179.5 KiB libssh i686 0.10.6-8.fc41 local 547.3 KiB libssh-config noarch 0.10.6-8.fc41 local 277.0 B libstdc++ i686 14.2.1-7.fc41 local 2.7 MiB libtasn1 i686 4.19.0-9.fc41 local 179.0 KiB libtirpc i686 1.3.6-1.rc3.fc41 local 208.6 KiB libtool-ltdl i686 2.4.7-12.fc41 local 69.4 KiB libunistring i686 1.1-8.fc41 local 1.7 MiB libutempter i686 1.2.1-15.fc41 local 56.2 KiB libuuid i686 2.40.4-1.fc41 local 39.1 KiB libverto i686 0.3.2-9.fc41 local 28.8 KiB libxcrypt i686 4.4.38-3.fc41 local 281.1 KiB libxml2 i686 2.12.9-1.fc41 local 1.8 MiB libzstd i686 1.5.6-2.fc41 local 727.1 KiB lua-libs i686 5.4.6-6.fc41 local 308.6 KiB lua-srpm-macros noarch 1-14.fc41 local 1.3 KiB lz4-libs i686 1.10.0-1.fc41 local 144.8 KiB mpfr i686 4.2.1-5.fc41 local 966.6 KiB ncurses-base noarch 6.5-2.20240629.fc41 local 326.3 KiB ncurses-libs i686 6.5-2.20240629.fc41 local 971.0 KiB ocaml-srpm-macros noarch 10-3.fc41 local 1.9 KiB openblas-srpm-macros noarch 2-18.fc41 local 112.0 B openldap i686 2.6.8-7.fc41 local 664.2 KiB openssl-libs i686 1:3.2.2-11.fc41 local 6.1 MiB p11-kit i686 0.25.5-3.fc41 local 2.3 MiB p11-kit-trust i686 0.25.5-3.fc41 local 361.6 KiB package-notes-srpm-macros noarch 0.5-12.fc41 local 1.6 KiB pam i686 1.6.1-7.fc41 local 1.8 MiB pam-libs i686 1.6.1-7.fc41 local 132.7 KiB pcre2 i686 10.44-1.fc41.1 local 660.1 KiB pcre2-syntax noarch 10.44-1.fc41.1 local 251.6 KiB perl-srpm-macros noarch 1-56.fc41 local 861.0 B pkgconf i686 2.3.0-1.fc41 local 87.0 KiB pkgconf-m4 noarch 2.3.0-1.fc41 local 14.4 KiB pkgconf-pkg-config i686 2.3.0-1.fc41 local 979.0 B popt i686 1.19-7.fc41 local 136.0 KiB publicsuffix-list-dafsa noarch 20240107-4.fc41 local 67.5 KiB pyproject-srpm-macros noarch 1.16.4-1.fc41 local 1.9 KiB python-srpm-macros noarch 3.13-3.fc41 local 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc41 local 500.0 B qt6-srpm-macros noarch 6.8.1-4.fc41 local 456.0 B readline i686 8.2-10.fc41 local 465.5 KiB rpm i686 4.20.0-1.fc41 local 3.0 MiB rpm-build-libs i686 4.20.0-1.fc41 local 209.4 KiB rpm-libs i686 4.20.0-1.fc41 local 768.8 KiB rpm-sequoia i686 1.7.0-3.fc41 local 2.6 MiB rust-srpm-macros noarch 26.3-3.fc41 local 4.8 KiB setup noarch 2.15.0-8.fc41 local 720.7 KiB sqlite-libs i686 3.46.1-2.fc41 local 1.5 MiB systemd-libs i686 256.11-1.fc41 local 2.0 MiB util-linux-core i686 2.40.4-1.fc41 local 1.4 MiB xxhash-libs i686 0.8.3-1.fc41 local 111.7 KiB xz-libs i686 1:5.6.2-2.fc41 local 229.8 KiB zig-srpm-macros noarch 1-3.fc41 local 1.1 KiB zip i686 3.0-41.fc41 local 707.1 KiB zlib-ng-compat i686 2.2.3-1.fc41 local 157.7 KiB zstd i686 1.5.6-2.fc41 local 1.6 MiB Installing groups: build Transaction Summary: Installing: 154 packages Total size of inbound packages is 52 MiB. Need to download 0 B. After this operation, 176 MiB extra will be used (install 176 MiB, remove 0 B). [1/1] bash-0:5.2.32-1.fc41.i686 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [1/1] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/2] shadow-utils-2:4.15.1-12.fc41.i68 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [2/2] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/3] coreutils-0:9.5-11.fc41.i686 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [3/3] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/4] fedora-release-0:41-29.noarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [4/4] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/5] util-linux-0:2.40.4-1.fc41.i686 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded 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tar-2:1.35-4.fc41.i686 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [10/10] Total 100% | 0.0 B/s | 0.0 B | 00m00s [ 1/11] unzip-0:6.0-64.fc41.i686 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [11/11] Total 100% | 0.0 B/s | 0.0 B | 00m00s [ 1/12] which-0:2.21-42.fc41.i686 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [12/12] Total 100% | 0.0 B/s | 0.0 B | 00m00s [ 1/13] bzip2-0:1.0.8-19.fc41.i686 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [13/13] Total 100% | 0.0 B/s | 0.0 B | 00m00s [ 1/14] cpio-0:2.15-2.fc41.i686 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded 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downloaded -------------------------------------------------------------------------------- [149/149] Total 100% | 0.0 B/s | 0.0 B | 00m00s [ 1/150] publicsuffix-list-dafsa-0:202 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [150/150] Total 100% | 0.0 B/s | 0.0 B | 00m00s [ 1/151] libssh-config-0:0.10.6-8.fc41 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [151/151] Total 100% | 0.0 B/s | 0.0 B | 00m00s [ 1/152] cyrus-sasl-lib-0:2.1.28-27.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [152/152] Total 100% | 0.0 B/s | 0.0 B | 00m00s [ 1/153] libevent-0:2.1.12-14.fc41.i68 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [153/153] Total 100% | 0.0 B/s | 0.0 B | 00m00s [ 1/154] libtool-ltdl-0:2.4.7-12.fc41. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [154/154] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction [ 1/156] Verify package files 100% | 993.0 B/s | 154.0 B | 00m00s [ 2/156] Prepare transaction 100% | 4.3 KiB/s | 154.0 B | 00m00s [ 3/156] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 4/156] Installing publicsuffix-list- 100% | 0.0 B/s | 68.3 KiB | 00m00s [ 5/156] Installing fedora-release-ide 100% | 0.0 B/s | 940.0 B | 00m00s [ 6/156] Installing fedora-gpg-keys-0: 100% | 56.1 MiB/s | 172.2 KiB | 00m00s [ 7/156] Installing fedora-repos-0:41- 100% | 0.0 B/s | 5.7 KiB | 00m00s [ 8/156] Installing fedora-release-com 100% | 23.4 MiB/s | 24.0 KiB | 00m00s [ 9/156] Installing fedora-release-0:4 100% | 0.0 B/s | 124.0 B | 00m00s [ 10/156] Installing setup-0:2.15.0-8.f 100% | 71.0 MiB/s | 726.5 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 11/156] Installing filesystem-0:3.18- 100% | 3.8 MiB/s | 212.0 KiB | 00m00s [ 12/156] Installing basesystem-0:11-21 100% | 0.0 B/s | 124.0 B | 00m00s [ 13/156] Installing pcre2-syntax-0:10. 100% | 248.1 MiB/s | 254.1 KiB | 00m00s [ 14/156] Installing pkgconf-m4-0:2.3.0 100% | 0.0 B/s | 14.8 KiB | 00m00s [ 15/156] Installing ncurses-base-0:6.5 100% | 114.5 MiB/s | 351.7 KiB | 00m00s [ 16/156] Installing rust-srpm-macros-0 100% | 0.0 B/s | 5.6 KiB | 00m00s [ 17/156] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 732.0 B | 00m00s [ 18/156] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [ 19/156] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [ 20/156] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [ 21/156] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [ 22/156] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s [ 23/156] Installing 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build-reproducibil 100% | 0.0 B/s | 1.0 KiB | 00m00s [110/156] Installing sqlite-libs-0:3.46 100% | 385.8 MiB/s | 1.5 MiB | 00m00s [111/156] Installing rpm-libs-0:4.20.0- 100% | 376.2 MiB/s | 770.4 KiB | 00m00s [112/156] Installing ed-0:1.20.2-2.fc41 100% | 140.6 MiB/s | 144.0 KiB | 00m00s [113/156] Installing patch-0:2.7.6-25.f 100% | 292.5 MiB/s | 299.5 KiB | 00m00s [114/156] Installing cpio-0:2.15-2.fc41 100% | 276.3 MiB/s | 1.1 MiB | 00m00s [115/156] Installing diffutils-0:3.10-8 100% | 319.0 MiB/s | 1.6 MiB | 00m00s [116/156] Installing jansson-0:2.13.1-1 100% | 86.9 MiB/s | 89.0 KiB | 00m00s [117/156] Installing libgomp-0:14.2.1-7 100% | 502.5 MiB/s | 514.5 KiB | 00m00s [118/156] Installing rpm-build-libs-0:4 100% | 205.3 MiB/s | 210.2 KiB | 00m00s [119/156] Installing json-c-0:0.17-4.fc 100% | 0.0 B/s | 90.9 KiB | 00m00s [120/156] Installing libpkgconf-0:2.3.0 100% | 0.0 B/s | 81.8 KiB | 00m00s [121/156] Installing pkgconf-0:2.3.0-1. 100% | 87.4 MiB/s | 89.5 KiB | 00m00s 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| 00m00s [135/156] Installing libcurl-0:8.9.1-3. 100% | 409.2 MiB/s | 838.0 KiB | 00m00s [136/156] Installing elfutils-debuginfo 100% | 80.2 MiB/s | 82.1 KiB | 00m00s [137/156] Installing binutils-0:2.43.1- 100% | 428.9 MiB/s | 25.3 MiB | 00m00s [138/156] Installing elfutils-0:0.192-7 100% | 369.3 MiB/s | 2.6 MiB | 00m00s [139/156] Installing gdb-minimal-0:15.2 100% | 430.1 MiB/s | 13.3 MiB | 00m00s [140/156] Installing debugedit-0:5.1-4. 100% | 201.2 MiB/s | 206.0 KiB | 00m00s [141/156] Installing curl-0:8.9.1-3.fc4 100% | 86.7 MiB/s | 799.1 KiB | 00m00s [142/156] Installing rpm-0:4.20.0-1.fc4 100% | 207.1 MiB/s | 2.5 MiB | 00m00s [143/156] Installing efi-srpm-macros-0: 100% | 0.0 B/s | 41.2 KiB | 00m00s [144/156] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [145/156] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s [146/156] Installing fonts-srpm-macros- 100% | 0.0 B/s | 57.0 KiB | 00m00s [147/156] Installing forge-srpm-macros- 100% | 0.0 B/s | 40.3 KiB | 00m00s [148/156] Installing go-srpm-macros-0:3 100% | 0.0 B/s | 62.0 KiB | 00m00s [149/156] Installing python-srpm-macros 100% | 0.0 B/s | 52.2 KiB | 00m00s [150/156] Installing redhat-rpm-config- 100% | 185.6 MiB/s | 190.1 KiB | 00m00s [151/156] Installing rpm-build-0:4.20.0 100% | 91.2 MiB/s | 186.9 KiB | 00m00s [152/156] Installing pyproject-srpm-mac 100% | 2.4 MiB/s | 2.5 KiB | 00m00s [153/156] Installing util-linux-0:2.40. 100% | 187.5 MiB/s | 3.6 MiB | 00m00s [154/156] Installing authselect-0:1.5.0 100% | 80.6 MiB/s | 165.0 KiB | 00m00s [155/156] Installing which-0:2.21-42.fc 100% | 79.2 MiB/s | 81.1 KiB | 00m00s [156/156] Installing info-0:7.1-3.fc41. 100% | 329.2 KiB/s | 360.8 KiB | 00m01s Warning: skipped OpenPGP checks for 154 packages from repository: local Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.3.6-3.fc41.i686 alternatives-1.31-1.fc41.i686 ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.3-1.fc41.i686 authselect-1.5.0-8.fc41.i686 authselect-libs-1.5.0-8.fc41.i686 basesystem-11-21.fc41.noarch bash-5.2.32-1.fc41.i686 binutils-2.43.1-5.fc41.i686 build-reproducibility-srpm-macros-0.3.6-3.fc41.noarch bzip2-1.0.8-19.fc41.i686 bzip2-libs-1.0.8-19.fc41.i686 ca-certificates-2024.2.69_v8.0.401-1.0.fc41.noarch coreutils-9.5-11.fc41.i686 coreutils-common-9.5-11.fc41.i686 cpio-2.15-2.fc41.i686 cracklib-2.9.11-6.fc41.i686 crypto-policies-20241029-1.git8baf557.fc41.noarch curl-8.9.1-3.fc41.i686 cyrus-sasl-lib-2.1.28-27.fc41.i686 debugedit-5.1-4.fc41.i686 diffutils-3.10-8.fc41.i686 dwz-0.15-8.fc41.i686 ed-1.20.2-2.fc41.i686 efi-srpm-macros-5-13.fc41.noarch elfutils-0.192-7.fc41.i686 elfutils-debuginfod-client-0.192-7.fc41.i686 elfutils-default-yama-scope-0.192-7.fc41.noarch elfutils-libelf-0.192-7.fc41.i686 elfutils-libs-0.192-7.fc41.i686 fedora-gpg-keys-41-1.noarch fedora-release-41-29.noarch fedora-release-common-41-29.noarch fedora-release-identity-basic-41-29.noarch fedora-repos-41-1.noarch file-5.45-7.fc41.i686 file-libs-5.45-7.fc41.i686 filesystem-3.18-23.fc41.i686 findutils-4.10.0-4.fc41.i686 fonts-srpm-macros-2.0.5-17.fc41.noarch forge-srpm-macros-0.4.0-1.fc41.noarch fpc-srpm-macros-1.3-13.fc41.noarch gawk-5.3.0-4.fc41.i686 gdb-minimal-15.2-4.fc41.i686 gdbm-1.23-7.fc41.i686 gdbm-libs-1.23-7.fc41.i686 ghc-srpm-macros-1.9.1-2.fc41.noarch glibc-2.40-17.fc41.i686 glibc-common-2.40-17.fc41.i686 glibc-gconv-extra-2.40-17.fc41.i686 glibc-minimal-langpack-2.40-17.fc41.i686 gmp-6.3.0-2.fc41.i686 gnat-srpm-macros-6-6.fc41.noarch go-srpm-macros-3.6.0-5.fc41.noarch grep-3.11-9.fc41.i686 gzip-1.13-2.fc41.i686 info-7.1-3.fc41.i686 jansson-2.13.1-10.fc41.i686 json-c-0.17-4.fc41.i686 kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc41.i686 krb5-libs-1.21.3-3.fc41.i686 libacl-2.3.2-2.fc41.i686 libarchive-3.7.4-4.fc41.i686 libattr-2.5.2-4.fc41.i686 libblkid-2.40.4-1.fc41.i686 libbrotli-1.1.0-5.fc41.i686 libcap-2.70-4.fc41.i686 libcap-ng-0.8.5-3.fc41.i686 libcom_err-1.47.1-6.fc41.i686 libcurl-8.9.1-3.fc41.i686 libeconf-0.6.2-3.fc41.i686 libevent-2.1.12-14.fc41.i686 libfdisk-2.40.4-1.fc41.i686 libffi-3.4.6-3.fc41.i686 libgcc-14.2.1-7.fc41.i686 libgomp-14.2.1-7.fc41.i686 libidn2-2.3.7-2.fc41.i686 libmount-2.40.4-1.fc41.i686 libnghttp2-1.62.1-2.fc41.i686 libnsl2-2.0.1-2.fc41.i686 libpkgconf-2.3.0-1.fc41.i686 libpsl-0.21.5-4.fc41.i686 libpwquality-1.4.5-11.fc41.i686 libselinux-3.7-5.fc41.i686 libsemanage-3.7-2.fc41.i686 libsepol-3.7-2.fc41.i686 libsmartcols-2.40.4-1.fc41.i686 libssh-0.10.6-8.fc41.i686 libssh-config-0.10.6-8.fc41.noarch libstdc++-14.2.1-7.fc41.i686 libtasn1-4.19.0-9.fc41.i686 libtirpc-1.3.6-1.rc3.fc41.i686 libtool-ltdl-2.4.7-12.fc41.i686 libunistring-1.1-8.fc41.i686 libutempter-1.2.1-15.fc41.i686 libuuid-2.40.4-1.fc41.i686 libverto-0.3.2-9.fc41.i686 libxcrypt-4.4.38-3.fc41.i686 libxml2-2.12.9-1.fc41.i686 libzstd-1.5.6-2.fc41.i686 lua-libs-5.4.6-6.fc41.i686 lua-srpm-macros-1-14.fc41.noarch lz4-libs-1.10.0-1.fc41.i686 mpfr-4.2.1-5.fc41.i686 ncurses-base-6.5-2.20240629.fc41.noarch ncurses-libs-6.5-2.20240629.fc41.i686 ocaml-srpm-macros-10-3.fc41.noarch openblas-srpm-macros-2-18.fc41.noarch openldap-2.6.8-7.fc41.i686 openssl-libs-3.2.2-11.fc41.i686 p11-kit-0.25.5-3.fc41.i686 p11-kit-trust-0.25.5-3.fc41.i686 package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.6.1-7.fc41.i686 pam-libs-1.6.1-7.fc41.i686 patch-2.7.6-25.fc41.i686 pcre2-10.44-1.fc41.1.i686 pcre2-syntax-10.44-1.fc41.1.noarch perl-srpm-macros-1-56.fc41.noarch pkgconf-2.3.0-1.fc41.i686 pkgconf-m4-2.3.0-1.fc41.noarch pkgconf-pkg-config-2.3.0-1.fc41.i686 popt-1.19-7.fc41.i686 publicsuffix-list-dafsa-20240107-4.fc41.noarch pyproject-srpm-macros-1.16.4-1.fc41.noarch python-srpm-macros-3.13-3.fc41.noarch qt5-srpm-macros-5.15.15-1.fc41.noarch qt6-srpm-macros-6.8.1-4.fc41.noarch readline-8.2-10.fc41.i686 redhat-rpm-config-293-1.fc41.noarch rpm-4.20.0-1.fc41.i686 rpm-build-4.20.0-1.fc41.i686 rpm-build-libs-4.20.0-1.fc41.i686 rpm-libs-4.20.0-1.fc41.i686 rpm-sequoia-1.7.0-3.fc41.i686 rust-srpm-macros-26.3-3.fc41.noarch sed-4.9-3.fc41.i686 setup-2.15.0-8.fc41.noarch shadow-utils-4.15.1-12.fc41.i686 sqlite-libs-3.46.1-2.fc41.i686 systemd-libs-256.11-1.fc41.i686 tar-1.35-4.fc41.i686 unzip-6.0-64.fc41.i686 util-linux-2.40.4-1.fc41.i686 util-linux-core-2.40.4-1.fc41.i686 which-2.21-42.fc41.i686 xxhash-libs-0.8.3-1.fc41.i686 xz-5.6.2-2.fc41.i686 xz-libs-5.6.2-2.fc41.i686 zig-srpm-macros-1-3.fc41.noarch zip-3.0-41.fc41.i686 zlib-ng-compat-2.2.3-1.fc41.i686 zstd-1.5.6-2.fc41.i686 Start: buildsrpm Start: rpmbuild -bs Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1736985600 Wrote: /builddir/build/SRPMS/bcftools-1.15.1-11.fc41.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-41-i686-1737371804.483416/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-fkz6_ucv/bcftools/bcftools.spec) Config(child) 0 minutes 8 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/bcftools-1.15.1-11.fc41.src.rpm) Config(fedora-41-i686) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-41-i686-bootstrap-1737371804.483416/root. INFO: reusing tmpfs at /var/lib/mock/fedora-41-i686-bootstrap-1737371804.483416/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-41-i686-1737371804.483416/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.20.0-1.fc41.x86_64 rpm-sequoia-1.7.0-3.fc41.x86_64 dnf5-5.2.8.1-3.fc41.x86_64 dnf5-plugins-5.2.8.1-3.fc41.x86_64 Finish: chroot init Start: build phase for bcftools-1.15.1-11.fc41.src.rpm Start: build setup for bcftools-1.15.1-11.fc41.src.rpm Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1736985600 Wrote: /builddir/build/SRPMS/bcftools-1.15.1-11.fc41.src.rpm Updating and loading repositories: local 100% | 218.4 KiB/s | 3.5 KiB | 00m00s Copr repository 100% | 117.1 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: gcc i686 14.2.1-7.fc41 local 101.0 MiB gsl-devel i686 2.7.1-11.fc41 local 1.6 MiB htslib-devel i686 1.15.1-6.fc41 local 411.0 KiB htslib-tools i686 1.15.1-6.fc41 local 2.6 MiB make i686 1:4.4.1-8.fc41 local 1.8 MiB perl-ExtUtils-Embed noarch 1.35-515.fc41 copr_base 15.5 KiB perl-File-Temp noarch 1:0.231.100-511.fc41 local 162.3 KiB perl-FindBin noarch 1.54-515.fc41 copr_base 6.7 KiB perl-Getopt-Long noarch 1:2.58-2.fc41 local 144.5 KiB perl-interpreter i686 4:5.40.1-515.fc41 copr_base 121.5 KiB zlib-ng-compat-devel i686 2.2.3-1.fc41 local 107.0 KiB Installing dependencies: annobin-docs noarch 12.69-1.fc41 local 97.7 KiB annobin-plugin-gcc i686 12.69-1.fc41 local 984.1 KiB autoconf noarch 2.72-3.fc41 local 2.8 MiB automake noarch 1.16.5-17.fc41 local 1.7 MiB cmake-filesystem i686 3.30.5-1.fc41 local 0.0 B cpp i686 14.2.1-7.fc41 local 35.2 MiB emacs-filesystem noarch 1:30.0-3.fc41 local 0.0 B expat i686 2.6.4-1.fc41 local 295.5 KiB gcc-plugin-annobin i686 14.2.1-7.fc41 local 54.3 KiB glibc-devel i686 2.40-17.fc41 local 2.2 MiB groff-base i686 1.23.0-7.fc41 local 3.8 MiB gsl i686 2.7.1-11.fc41 local 3.6 MiB htslib i686 1.15.1-6.fc41 local 1.2 MiB kernel-headers i686 6.12.4-200.fc41 local 6.4 MiB libasan i686 14.2.1-7.fc41 local 1.7 MiB libatomic i686 14.2.1-7.fc41 local 25.5 KiB libb2 i686 0.98.1-12.fc41 local 53.4 KiB libmpc i686 1.3.1-6.fc41 local 168.0 KiB libubsan i686 14.2.1-7.fc41 local 523.8 KiB libxcrypt-devel i686 4.4.38-3.fc41 local 30.8 KiB m4 i686 1.4.19-10.fc41 local 596.2 KiB mpdecimal i686 2.5.1-16.fc41 local 204.1 KiB ncurses i686 6.5-2.20240629.fc41 local 613.4 KiB perl-AutoLoader noarch 5.74-515.fc41 copr_base 20.5 KiB perl-AutoSplit noarch 5.74-515.fc41 copr_base 23.1 KiB perl-B i686 1.89-515.fc41 copr_base 505.4 KiB perl-Benchmark noarch 1.25-515.fc41 copr_base 36.3 KiB perl-Carp noarch 1.54-511.fc41 local 46.6 KiB perl-Class-Struct noarch 0.68-515.fc41 copr_base 25.4 KiB perl-Data-Dumper i686 2.189-512.fc41 local 119.0 KiB perl-Devel-PPPort i686 3.72-512.fc41 local 915.8 KiB perl-Digest noarch 1.20-511.fc41 local 35.3 KiB perl-Digest-MD5 i686 2.59-5.fc41 local 59.1 KiB perl-DynaLoader i686 1.56-515.fc41 copr_base 32.1 KiB perl-Encode i686 4:3.21-511.fc41 local 3.3 MiB perl-Errno i686 1.38-515.fc41 copr_base 8.3 KiB perl-Exporter noarch 5.78-511.fc41 local 54.3 KiB perl-ExtUtils-Command noarch 2:7.70-512.fc41 local 9.6 KiB perl-ExtUtils-Constant noarch 0.25-515.fc41 copr_base 85.8 KiB perl-ExtUtils-Install noarch 2.22-511.fc41 local 85.5 KiB perl-ExtUtils-MakeMaker noarch 2:7.70-512.fc41 local 734.1 KiB perl-ExtUtils-Manifest noarch 1:1.75-511.fc41 local 84.8 KiB perl-ExtUtils-ParseXS noarch 1:3.51-511.fc41 local 399.7 KiB perl-Fcntl i686 1.18-515.fc41 copr_base 44.3 KiB perl-File-Basename noarch 2.86-515.fc41 copr_base 14.0 KiB perl-File-Compare noarch 1.100.800-515.fc41 copr_base 5.6 KiB perl-File-Copy noarch 2.41-515.fc41 copr_base 19.6 KiB perl-File-Find noarch 1.44-515.fc41 copr_base 41.9 KiB perl-File-Path noarch 2.18-511.fc41 local 63.5 KiB perl-File-stat noarch 1.14-515.fc41 copr_base 12.5 KiB perl-FileHandle noarch 2.05-515.fc41 copr_base 9.3 KiB perl-Getopt-Std noarch 1.14-515.fc41 copr_base 11.2 KiB perl-HTTP-Tiny noarch 0.090-1.fc41 local 154.4 KiB perl-IO i686 1.55-515.fc41 copr_base 146.4 KiB perl-IO-Socket-IP noarch 0.43-1.fc41 local 100.3 KiB perl-IO-Socket-SSL noarch 2.089-1.fc41 local 703.3 KiB perl-IPC-Open3 noarch 1.22-515.fc41 copr_base 22.5 KiB perl-MIME-Base32 noarch 1.303-21.fc41 local 30.7 KiB perl-MIME-Base64 i686 3.16-511.fc41 local 45.4 KiB perl-Net-SSLeay i686 1.94-7.fc41 local 1.4 MiB perl-POSIX i686 2.20-515.fc41 copr_base 234.5 KiB perl-PathTools i686 3.91-511.fc41 local 175.3 KiB perl-Pod-Escapes noarch 1:1.07-511.fc41 local 24.9 KiB perl-Pod-Perldoc noarch 3.28.01-512.fc41 local 163.7 KiB perl-Pod-Simple noarch 1:3.45-511.fc41 local 560.9 KiB perl-Pod-Usage noarch 4:2.03-511.fc41 local 84.8 KiB perl-Scalar-List-Utils i686 5:1.68-1.fc41 local 152.2 KiB perl-SelectSaver noarch 1.02-515.fc41 copr_base 2.2 KiB perl-Socket i686 4:2.038-511.fc41 local 115.3 KiB perl-Storable i686 1:3.32-511.fc41 local 231.7 KiB perl-Symbol noarch 1.09-515.fc41 copr_base 6.8 KiB perl-Term-ANSIColor noarch 5.01-512.fc41 local 97.5 KiB perl-Term-Cap noarch 1.18-511.fc41 local 29.3 KiB perl-Test-Harness noarch 1:3.50-1.fc41 local 559.6 KiB perl-Text-ParseWords noarch 3.31-511.fc41 local 13.6 KiB perl-Text-Tabs+Wrap noarch 2024.001-511.fc41 local 22.6 KiB perl-Thread-Queue noarch 3.14-511.fc41 local 28.9 KiB perl-Time-Local noarch 2:1.350-511.fc41 local 69.0 KiB perl-URI noarch 5.30-1.fc41 local 256.9 KiB perl-base noarch 2.27-515.fc41 copr_base 12.5 KiB perl-constant noarch 1.33-512.fc41 local 26.2 KiB perl-devel i686 4:5.40.1-515.fc41 copr_base 8.0 MiB perl-if noarch 0.61.000-515.fc41 copr_base 5.8 KiB perl-lib i686 0.65-515.fc41 copr_base 8.5 KiB perl-libnet noarch 3.15-512.fc41 local 289.4 KiB perl-libs i686 4:5.40.1-515.fc41 copr_base 10.1 MiB perl-locale noarch 1.12-515.fc41 copr_base 6.5 KiB perl-mro i686 1.29-515.fc41 copr_base 40.9 KiB perl-overload noarch 1.37-515.fc41 copr_base 71.5 KiB perl-overloading noarch 0.02-515.fc41 copr_base 4.8 KiB perl-parent noarch 1:0.242-1.fc41 local 10.0 KiB perl-podlators noarch 1:6.0.2-2.fc41 local 317.5 KiB perl-threads i686 1:2.40-511.fc41 local 114.5 KiB perl-threads-shared i686 1.69-511.fc41 local 87.0 KiB perl-vars noarch 1.05-515.fc41 copr_base 3.9 KiB perl-version i686 9:0.99.33-1.fc41 local 136.1 KiB python-pip-wheel noarch 24.2-1.fc41 local 1.2 MiB python3 i686 3.13.1-2.fc41 local 29.8 KiB python3-libs i686 3.13.1-2.fc41 local 39.9 MiB python3-pyparsing noarch 3.1.2-7.fc41 local 1.0 MiB systemtap-sdt-devel i686 5.2-1.fc41 local 182.4 KiB systemtap-sdt-dtrace i686 5.2-1.fc41 local 179.0 KiB tzdata noarch 2024b-1.fc41 local 1.6 MiB Transaction Summary: Installing: 114 packages Total size of inbound packages is 78 MiB. Need to download 3 MiB. After this operation, 245 MiB extra will be used (install 245 MiB, remove 0 B). [1/1] gcc-0:14.2.1-7.fc41.i686 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [1/1] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/5] make-1:4.4.1-8.fc41.i686 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [2/6] perl-File-Temp-1:0.231.100-511.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [3/7] perl-Getopt-Long-1:2.58-2.fc41.no 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [4/8] zlib-ng-compat-devel-0:2.2.3-1.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [5/9] perl-ExtUtils-Embed-0:1.35-515.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 6/11] perl-interpreter-4:5.40.1-515.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 7/12] cpp-0:14.2.1-7.fc41.i686 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 8/13] glibc-devel-0:2.40-17.fc41.i686 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 9/14] libasan-0:14.2.1-7.fc41.i686 100% | 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repositories: copr_base, local Complete! Finish: build setup for bcftools-1.15.1-11.fc41.src.rpm Start: rpmbuild bcftools-1.15.1-11.fc41.src.rpm Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1736985600 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.xT4gYW + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + test -d /builddir/build/BUILD/bcftools-1.15.1-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/bcftools-1.15.1-build + /usr/bin/rm -rf /builddir/build/BUILD/bcftools-1.15.1-build + /usr/bin/mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build + /usr/bin/mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.RIv3tX + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + cd /builddir/build/BUILD/bcftools-1.15.1-build + rm -rf bcftools-1.15.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/bcftools-1.15.1.tar.bz2 + STATUS=0 + '[' 0 -ne 0 ']' + cd bcftools-1.15.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (bcftools-1.15.1-aarch64-fix-vcf_plugin-tests.patch): + echo 'Patch #0 (bcftools-1.15.1-aarch64-fix-vcf_plugin-tests.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file plugins/fill-tags.c + sed -i '1s|/usr/bin/env perl|/usr/bin/perl|' misc/color-chrs.pl misc/demo-flt.pl misc/run-roh.pl misc/vcfutils.pl misc/plot-vcfstats + sed -i '1s|/usr/bin/env python3\{0,1\}|/usr/bin/python3|' misc/gff2gff.py misc/guess-ploidy.py misc/plot-roh.py + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.FeRdwK + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bcftools-1.15.1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/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' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure --- ./htslib-1.15.1/configure.backup 2022-04-07 15:42:52.000000000 +0000 +++ ./htslib-1.15.1/configure 2025-01-20 11:16:58.968601477 +0000 @@ -1697,7 +1697,7 @@ #ifdef __cplusplus extern "C" #endif -char $2 (); +__attribute__ ((used)) char $2 (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=i686-redhat-linux --host=i686-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --with-htslib=system --enable-perl-filters --enable-libgsl '--with-bcf-plugin-path=/usr/local/libexec/bcftools:$(plugindir)' checking for i686-redhat-linux-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 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 -j4 V=1 VERBOSE=1 echo '#define BCFTOOLS_VERSION "1.15.1"' > version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o tabix.o tabix.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfindex.o vcfindex.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfisec.o vcfisec.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfquery.o vcfquery.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcffilter.o vcffilter.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfstats.o vcfstats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfsom.o vcfsom.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfgtcheck.o vcfgtcheck.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfview.o vcfview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfmerge.o vcfmerge.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfnorm.o vcfnorm.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfroh.o vcfroh.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfconcat.o vcfconcat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcmp.o vcmp.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o gvcf.o gvcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfcall.o vcfcall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o mcall.o mcall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o reheader.o reheader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfannotate.o vcfannotate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o tsv2vcf.o tsv2vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfhead.o vcfhead.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o HMM.o HMM.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfcnv.o vcfcnv.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o convert.o convert.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfconvert.o vcfconvert.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o ploidy.o ploidy.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bin.o bin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o version.o version.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o hclust.o hclust.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o consensus.o consensus.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o smpl_ilist.o smpl_ilist.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfbuf.o vcfbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o mpileup.o mpileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bam2bcf.o bam2bcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o cols.o cols.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfsort.o vcfsort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o dist.o dist.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bam_sample.o bam_sample.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o extsort.o extsort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o em.o em.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o ccall.o ccall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o kmin.o kmin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o str_finder.o str_finder.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o abuf.o abuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o prob1.o prob1.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o peakfit.o peakfit.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o polysomy.o polysomy.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o csq.o csq.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 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-mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 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-msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall 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-mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-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,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/test-rbuf test/test-rbuf.o -lz gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o polysomy.o peakfit.o vcfplugin.o -lhts -lm -lz -lgsl -lgslcblas -Wl,--enable-new-dtags -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -fstack-protector-strong -L/usr/local/lib -L/usr/lib/perl5/CORE -lperl -lpthread -lresolv -ldl -lm -lcrypt -lutil -lc -lpthread + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.MAWhAf + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + '[' /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT ++ dirname /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT + mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build + mkdir /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bcftools-1.15.1 + /usr/bin/make install DESTDIR=/builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/bin /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/man/man1 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/libexec/bcftools /usr/bin/install -p bcftools /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/bin /usr/bin/install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/bin /usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/man/man1 /usr/bin/install -p plugins/*.so /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/libexec/bcftools + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.15.1-11.fc41 --unique-debug-suffix -1.15.1-11.fc41.i386 --unique-debug-src-base bcftools-1.15.1-11.fc41.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1 find-debuginfo: starting Extracting debug info from 39 files DWARF-compressing 39 files sepdebugcrcfix: Updated 39 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/bcftools-1.15.1-11.fc41.i386 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j4 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT Scanned 19 directories and 208 files, processed 0 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/bcftools-1.15.1-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.0Vcu1m + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bcftools-1.15.1 + ldd bcftools + grep -E '/lib(64)?/libhts\.so\.' libhts.so.3 => /lib/libhts.so.3 (0xf7cd4000) + sed -i -E '/^test_vcf_convert_hs2vcf.+convert.gs.gt.ids.3N6.gen.+/ s/^/#/' test/test.pl + 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_usage: bcftools ./test/test.pl: module IO::Pty not found; skipping usage tests test_tabix: tabix /tmp/UDLPM26cBc/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/UDLPM26cBc/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/UDLPM26cBc/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/UDLPM26cBc/merge.a.bcf 1:3000151-3000151 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/UDLPM26cBc/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/UDLPM26cBc/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/UDLPM26cBc/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/UDLPM26cBc/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/UDLPM26cBc/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/UDLPM26cBc/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/UDLPM26cBc/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/UDLPM26cBc/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/UDLPM26cBc/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/UDLPM26cBc/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/UDLPM26cBc/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/UDLPM26cBc/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/UDLPM26cBc/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/UDLPM26cBc/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/UDLPM26cBc/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/UDLPM26cBc/idx.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/UDLPM26cBc/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/UDLPM26cBc/idx.bcf.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/UDLPM26cBc/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/UDLPM26cBc/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/UDLPM26cBc/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/UDLPM26cBc/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/UDLPM26cBc/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/UDLPM26cBc/empty.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/UDLPM26cBc/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/UDLPM26cBc/empty.bcf.csi .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s - /tmp/UDLPM26cBc/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/misc/plot-vcfstats -m /tmp/UDLPM26cBc/check.1.chk /tmp/UDLPM26cBc/check.2.chk /tmp/UDLPM26cBc/check.3.chk /tmp/UDLPM26cBc/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s - /tmp/UDLPM26cBc/stats.a.vcf.gz /tmp/UDLPM26cBc/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s B /tmp/UDLPM26cBc/stats.a.vcf.gz /tmp/UDLPM26cBc/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s - /tmp/UDLPM26cBc/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n =2 /tmp/UDLPM26cBc/isec.a.vcf.gz /tmp/UDLPM26cBc/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n =2 /tmp/UDLPM26cBc/isec.a.vcf.gz /tmp/UDLPM26cBc/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/UDLPM26cBc/isec.a.vcf.gz /tmp/UDLPM26cBc/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/UDLPM26cBc/isec.a.vcf.gz /tmp/UDLPM26cBc/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n =2 -c both /tmp/UDLPM26cBc/isec.a.vcf.gz /tmp/UDLPM26cBc/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n =2 -c both /tmp/UDLPM26cBc/isec.a.vcf.gz /tmp/UDLPM26cBc/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n =2 -c any /tmp/UDLPM26cBc/isec.a.vcf.gz /tmp/UDLPM26cBc/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n =2 -c any /tmp/UDLPM26cBc/isec.a.vcf.gz /tmp/UDLPM26cBc/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -C -c any /tmp/UDLPM26cBc/isec.a.vcf.gz /tmp/UDLPM26cBc/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -C -c any /tmp/UDLPM26cBc/isec.a.vcf.gz /tmp/UDLPM26cBc/isec.b.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec --no-version -T /tmp/UDLPM26cBc/isec.tab.gz /tmp/UDLPM26cBc/isec.a.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -T /tmp/UDLPM26cBc/isec.tab.gz /tmp/UDLPM26cBc/isec.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/UDLPM26cBc/isec-miss.1.1.vcf.gz /tmp/UDLPM26cBc/isec-miss.1.2.vcf.gz /tmp/UDLPM26cBc/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/UDLPM26cBc/isec-miss.1.1.vcf.gz /tmp/UDLPM26cBc/isec-miss.1.2.vcf.gz /tmp/UDLPM26cBc/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/UDLPM26cBc/isec-miss.1.1.vcf.gz /tmp/UDLPM26cBc/isec-miss.1.2.vcf.gz /tmp/UDLPM26cBc/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/UDLPM26cBc/isec-miss.1.1.vcf.gz /tmp/UDLPM26cBc/isec-miss.1.2.vcf.gz /tmp/UDLPM26cBc/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/UDLPM26cBc/isec-miss.2.1.vcf.gz /tmp/UDLPM26cBc/isec-miss.2.2.vcf.gz /tmp/UDLPM26cBc/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/UDLPM26cBc/isec-miss.2.1.vcf.gz /tmp/UDLPM26cBc/isec-miss.2.2.vcf.gz /tmp/UDLPM26cBc/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/UDLPM26cBc/isec-miss.2.1.vcf.gz /tmp/UDLPM26cBc/isec-miss.2.2.vcf.gz /tmp/UDLPM26cBc/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/UDLPM26cBc/isec-miss.2.1.vcf.gz /tmp/UDLPM26cBc/isec-miss.2.2.vcf.gz /tmp/UDLPM26cBc/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AF:join /tmp/UDLPM26cBc/merge.join.a.vcf.gz /tmp/UDLPM26cBc/merge.join.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AF:join /tmp/UDLPM26cBc/merge.join.a.vcf.gz /tmp/UDLPM26cBc/merge.join.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AF:join /tmp/UDLPM26cBc/merge.join.a.bcf /tmp/UDLPM26cBc/merge.join.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AF:join /tmp/UDLPM26cBc/merge.join.a.bcf /tmp/UDLPM26cBc/merge.join.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/UDLPM26cBc/merge.LPL.a.vcf.gz /tmp/UDLPM26cBc/merge.LPL.b.vcf.gz /tmp/UDLPM26cBc/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/UDLPM26cBc/merge.LPL.a.vcf.gz /tmp/UDLPM26cBc/merge.LPL.b.vcf.gz /tmp/UDLPM26cBc/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/UDLPM26cBc/merge.LPL.a.bcf /tmp/UDLPM26cBc/merge.LPL.b.bcf /tmp/UDLPM26cBc/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/UDLPM26cBc/merge.LPL.a.bcf /tmp/UDLPM26cBc/merge.LPL.b.bcf /tmp/UDLPM26cBc/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 1 /tmp/UDLPM26cBc/merge.LPL.a.vcf.gz /tmp/UDLPM26cBc/merge.LPL.b.vcf.gz /tmp/UDLPM26cBc/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 1 /tmp/UDLPM26cBc/merge.LPL.a.vcf.gz /tmp/UDLPM26cBc/merge.LPL.b.vcf.gz /tmp/UDLPM26cBc/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 1 /tmp/UDLPM26cBc/merge.LPL.a.bcf /tmp/UDLPM26cBc/merge.LPL.b.bcf /tmp/UDLPM26cBc/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 1 /tmp/UDLPM26cBc/merge.LPL.a.bcf /tmp/UDLPM26cBc/merge.LPL.b.bcf /tmp/UDLPM26cBc/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 2 /tmp/UDLPM26cBc/merge.LPL.a.vcf.gz /tmp/UDLPM26cBc/merge.LPL.b.vcf.gz /tmp/UDLPM26cBc/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 2 /tmp/UDLPM26cBc/merge.LPL.a.vcf.gz /tmp/UDLPM26cBc/merge.LPL.b.vcf.gz /tmp/UDLPM26cBc/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 2 /tmp/UDLPM26cBc/merge.LPL.a.bcf /tmp/UDLPM26cBc/merge.LPL.b.bcf /tmp/UDLPM26cBc/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 2 /tmp/UDLPM26cBc/merge.LPL.a.bcf /tmp/UDLPM26cBc/merge.LPL.b.bcf /tmp/UDLPM26cBc/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 3 /tmp/UDLPM26cBc/merge.LPL.a.vcf.gz /tmp/UDLPM26cBc/merge.LPL.b.vcf.gz /tmp/UDLPM26cBc/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 3 /tmp/UDLPM26cBc/merge.LPL.a.vcf.gz /tmp/UDLPM26cBc/merge.LPL.b.vcf.gz /tmp/UDLPM26cBc/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 3 /tmp/UDLPM26cBc/merge.LPL.a.bcf /tmp/UDLPM26cBc/merge.LPL.b.bcf /tmp/UDLPM26cBc/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 3 /tmp/UDLPM26cBc/merge.LPL.a.bcf /tmp/UDLPM26cBc/merge.LPL.b.bcf /tmp/UDLPM26cBc/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 4 /tmp/UDLPM26cBc/merge.LPL.a.vcf.gz /tmp/UDLPM26cBc/merge.LPL.b.vcf.gz /tmp/UDLPM26cBc/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 4 /tmp/UDLPM26cBc/merge.LPL.a.vcf.gz /tmp/UDLPM26cBc/merge.LPL.b.vcf.gz /tmp/UDLPM26cBc/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 4 /tmp/UDLPM26cBc/merge.LPL.a.bcf /tmp/UDLPM26cBc/merge.LPL.b.bcf /tmp/UDLPM26cBc/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 4 /tmp/UDLPM26cBc/merge.LPL.a.bcf /tmp/UDLPM26cBc/merge.LPL.b.bcf /tmp/UDLPM26cBc/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 5 /tmp/UDLPM26cBc/merge.LPL.a.vcf.gz /tmp/UDLPM26cBc/merge.LPL.b.vcf.gz /tmp/UDLPM26cBc/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 5 /tmp/UDLPM26cBc/merge.LPL.a.vcf.gz /tmp/UDLPM26cBc/merge.LPL.b.vcf.gz /tmp/UDLPM26cBc/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 5 /tmp/UDLPM26cBc/merge.LPL.a.bcf /tmp/UDLPM26cBc/merge.LPL.b.bcf /tmp/UDLPM26cBc/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 5 /tmp/UDLPM26cBc/merge.LPL.a.bcf /tmp/UDLPM26cBc/merge.LPL.b.bcf /tmp/UDLPM26cBc/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/UDLPM26cBc/merge.a.vcf.gz /tmp/UDLPM26cBc/merge.b.vcf.gz /tmp/UDLPM26cBc/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/UDLPM26cBc/merge.a.vcf.gz /tmp/UDLPM26cBc/merge.b.vcf.gz /tmp/UDLPM26cBc/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/UDLPM26cBc/merge.a.bcf /tmp/UDLPM26cBc/merge.b.bcf /tmp/UDLPM26cBc/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/UDLPM26cBc/merge.a.bcf /tmp/UDLPM26cBc/merge.b.bcf /tmp/UDLPM26cBc/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -Fx /tmp/UDLPM26cBc/merge.a.vcf.gz /tmp/UDLPM26cBc/merge.b.vcf.gz /tmp/UDLPM26cBc/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -Fx /tmp/UDLPM26cBc/merge.a.vcf.gz /tmp/UDLPM26cBc/merge.b.vcf.gz /tmp/UDLPM26cBc/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -Fx /tmp/UDLPM26cBc/merge.a.bcf /tmp/UDLPM26cBc/merge.b.bcf /tmp/UDLPM26cBc/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -Fx /tmp/UDLPM26cBc/merge.a.bcf /tmp/UDLPM26cBc/merge.b.bcf /tmp/UDLPM26cBc/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -0 /tmp/UDLPM26cBc/merge.a.vcf.gz /tmp/UDLPM26cBc/merge.b.vcf.gz /tmp/UDLPM26cBc/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -0 /tmp/UDLPM26cBc/merge.a.vcf.gz /tmp/UDLPM26cBc/merge.b.vcf.gz /tmp/UDLPM26cBc/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -0 /tmp/UDLPM26cBc/merge.a.bcf /tmp/UDLPM26cBc/merge.b.bcf /tmp/UDLPM26cBc/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -0 /tmp/UDLPM26cBc/merge.a.bcf /tmp/UDLPM26cBc/merge.b.bcf /tmp/UDLPM26cBc/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m none /tmp/UDLPM26cBc/merge.2.a.vcf.gz /tmp/UDLPM26cBc/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m none /tmp/UDLPM26cBc/merge.2.a.vcf.gz /tmp/UDLPM26cBc/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m none /tmp/UDLPM26cBc/merge.2.a.bcf /tmp/UDLPM26cBc/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m none /tmp/UDLPM26cBc/merge.2.a.bcf /tmp/UDLPM26cBc/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m both /tmp/UDLPM26cBc/merge.2.a.vcf.gz /tmp/UDLPM26cBc/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m both /tmp/UDLPM26cBc/merge.2.a.vcf.gz /tmp/UDLPM26cBc/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m both /tmp/UDLPM26cBc/merge.2.a.bcf /tmp/UDLPM26cBc/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m both /tmp/UDLPM26cBc/merge.2.a.bcf /tmp/UDLPM26cBc/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m all /tmp/UDLPM26cBc/merge.2.a.vcf.gz /tmp/UDLPM26cBc/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m all /tmp/UDLPM26cBc/merge.2.a.vcf.gz /tmp/UDLPM26cBc/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m all /tmp/UDLPM26cBc/merge.2.a.bcf /tmp/UDLPM26cBc/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m all /tmp/UDLPM26cBc/merge.2.a.bcf /tmp/UDLPM26cBc/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/UDLPM26cBc/merge.3.a.vcf.gz /tmp/UDLPM26cBc/merge.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/UDLPM26cBc/merge.3.a.vcf.gz /tmp/UDLPM26cBc/merge.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/UDLPM26cBc/merge.3.a.bcf /tmp/UDLPM26cBc/merge.3.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/UDLPM26cBc/merge.3.a.bcf /tmp/UDLPM26cBc/merge.3.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m id /tmp/UDLPM26cBc/merge.4.a.vcf.gz /tmp/UDLPM26cBc/merge.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m id /tmp/UDLPM26cBc/merge.4.a.vcf.gz /tmp/UDLPM26cBc/merge.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m id /tmp/UDLPM26cBc/merge.4.a.bcf /tmp/UDLPM26cBc/merge.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m id /tmp/UDLPM26cBc/merge.4.a.bcf /tmp/UDLPM26cBc/merge.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/UDLPM26cBc/gvcf.merge.1.vcf.gz /tmp/UDLPM26cBc/gvcf.merge.2.vcf.gz /tmp/UDLPM26cBc/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/UDLPM26cBc/gvcf.merge.1.vcf.gz /tmp/UDLPM26cBc/gvcf.merge.2.vcf.gz /tmp/UDLPM26cBc/gvcf.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/UDLPM26cBc/gvcf.merge.1.bcf /tmp/UDLPM26cBc/gvcf.merge.2.bcf /tmp/UDLPM26cBc/gvcf.merge.3.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/UDLPM26cBc/gvcf.merge.1.bcf /tmp/UDLPM26cBc/gvcf.merge.2.bcf /tmp/UDLPM26cBc/gvcf.merge.3.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/UDLPM26cBc/merge.gvcf.2.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.2.b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/UDLPM26cBc/merge.gvcf.2.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.2.b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - -i SRC:join /tmp/UDLPM26cBc/merge.gvcf.3.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - -i SRC:join /tmp/UDLPM26cBc/merge.gvcf.3.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/UDLPM26cBc/merge.gvcf.4.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/UDLPM26cBc/merge.gvcf.4.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/UDLPM26cBc/merge.gvcf.4.a.bcf /tmp/UDLPM26cBc/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/UDLPM26cBc/merge.gvcf.4.a.bcf /tmp/UDLPM26cBc/merge.gvcf.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/UDLPM26cBc/merge.5.a.vcf.gz /tmp/UDLPM26cBc/merge.5.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/UDLPM26cBc/merge.5.a.vcf.gz /tmp/UDLPM26cBc/merge.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/UDLPM26cBc/merge.5.a.bcf /tmp/UDLPM26cBc/merge.5.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/UDLPM26cBc/merge.5.a.bcf /tmp/UDLPM26cBc/merge.5.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/UDLPM26cBc/merge.6.a.vcf.gz /tmp/UDLPM26cBc/merge.6.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/UDLPM26cBc/merge.6.a.vcf.gz /tmp/UDLPM26cBc/merge.6.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/UDLPM26cBc/merge.6.a.bcf /tmp/UDLPM26cBc/merge.6.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/UDLPM26cBc/merge.6.a.bcf /tmp/UDLPM26cBc/merge.6.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/UDLPM26cBc/merge.gvcf.7.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/UDLPM26cBc/merge.gvcf.7.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/UDLPM26cBc/merge.gvcf.7.a.bcf /tmp/UDLPM26cBc/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/UDLPM26cBc/merge.gvcf.7.a.bcf /tmp/UDLPM26cBc/merge.gvcf.7.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/UDLPM26cBc/merge.gvcf.8.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/UDLPM26cBc/merge.gvcf.8.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/UDLPM26cBc/merge.gvcf.8.a.bcf /tmp/UDLPM26cBc/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/UDLPM26cBc/merge.gvcf.8.a.bcf /tmp/UDLPM26cBc/merge.gvcf.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/UDLPM26cBc/merge.7.a.vcf.gz /tmp/UDLPM26cBc/merge.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/UDLPM26cBc/merge.7.a.vcf.gz /tmp/UDLPM26cBc/merge.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/UDLPM26cBc/merge.7.a.bcf /tmp/UDLPM26cBc/merge.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/UDLPM26cBc/merge.7.a.bcf /tmp/UDLPM26cBc/merge.7.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/UDLPM26cBc/merge.gvcf.9a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9c.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/UDLPM26cBc/merge.gvcf.9a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9c.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/UDLPM26cBc/merge.gvcf.9a.bcf /tmp/UDLPM26cBc/merge.gvcf.9b.bcf /tmp/UDLPM26cBc/merge.gvcf.9c.bcf /tmp/UDLPM26cBc/merge.gvcf.9d.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/UDLPM26cBc/merge.gvcf.9a.bcf /tmp/UDLPM26cBc/merge.gvcf.9b.bcf /tmp/UDLPM26cBc/merge.gvcf.9c.bcf /tmp/UDLPM26cBc/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/UDLPM26cBc/merge.gvcf.9a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9c.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/UDLPM26cBc/merge.gvcf.9a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9c.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/UDLPM26cBc/merge.gvcf.9a.bcf /tmp/UDLPM26cBc/merge.gvcf.9b.bcf /tmp/UDLPM26cBc/merge.gvcf.9c.bcf /tmp/UDLPM26cBc/merge.gvcf.9d.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/UDLPM26cBc/merge.gvcf.9a.bcf /tmp/UDLPM26cBc/merge.gvcf.9b.bcf /tmp/UDLPM26cBc/merge.gvcf.9c.bcf /tmp/UDLPM26cBc/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/UDLPM26cBc/merge.gvcf.9a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9c.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9d.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/UDLPM26cBc/merge.gvcf.9a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9c.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9d.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/UDLPM26cBc/merge.gvcf.9a.bcf /tmp/UDLPM26cBc/merge.gvcf.9b.bcf /tmp/UDLPM26cBc/merge.gvcf.9c.bcf /tmp/UDLPM26cBc/merge.gvcf.9d.bcf /tmp/UDLPM26cBc/merge.gvcf.9e.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/UDLPM26cBc/merge.gvcf.9a.bcf /tmp/UDLPM26cBc/merge.gvcf.9b.bcf /tmp/UDLPM26cBc/merge.gvcf.9c.bcf /tmp/UDLPM26cBc/merge.gvcf.9d.bcf /tmp/UDLPM26cBc/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/UDLPM26cBc/merge.gvcf.9a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9c.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9d.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/UDLPM26cBc/merge.gvcf.9a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9c.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9d.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/UDLPM26cBc/merge.gvcf.9a.bcf /tmp/UDLPM26cBc/merge.gvcf.9b.bcf /tmp/UDLPM26cBc/merge.gvcf.9c.bcf /tmp/UDLPM26cBc/merge.gvcf.9d.bcf /tmp/UDLPM26cBc/merge.gvcf.9e.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/UDLPM26cBc/merge.gvcf.9a.bcf /tmp/UDLPM26cBc/merge.gvcf.9b.bcf /tmp/UDLPM26cBc/merge.gvcf.9c.bcf /tmp/UDLPM26cBc/merge.gvcf.9d.bcf /tmp/UDLPM26cBc/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/UDLPM26cBc/merge.gvcf.10.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/UDLPM26cBc/merge.gvcf.10.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/UDLPM26cBc/merge.gvcf.10.a.bcf /tmp/UDLPM26cBc/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/UDLPM26cBc/merge.gvcf.10.a.bcf /tmp/UDLPM26cBc/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -m none /tmp/UDLPM26cBc/merge.gvcf.10.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -m none /tmp/UDLPM26cBc/merge.gvcf.10.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -m none /tmp/UDLPM26cBc/merge.gvcf.10.a.bcf /tmp/UDLPM26cBc/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -m none /tmp/UDLPM26cBc/merge.gvcf.10.a.bcf /tmp/UDLPM26cBc/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/UDLPM26cBc/merge.gvcf.10.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/UDLPM26cBc/merge.gvcf.10.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/UDLPM26cBc/merge.gvcf.10.a.bcf /tmp/UDLPM26cBc/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/UDLPM26cBc/merge.gvcf.10.a.bcf /tmp/UDLPM26cBc/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/UDLPM26cBc/merge.gvcf.10.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/UDLPM26cBc/merge.gvcf.10.a.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/UDLPM26cBc/merge.gvcf.10.a.bcf /tmp/UDLPM26cBc/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/UDLPM26cBc/merge.gvcf.10.a.bcf /tmp/UDLPM26cBc/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/UDLPM26cBc/merge.gvcf.10.b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/UDLPM26cBc/merge.gvcf.10.b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/UDLPM26cBc/merge.gvcf.10.b.bcf /tmp/UDLPM26cBc/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/UDLPM26cBc/merge.gvcf.10.b.bcf /tmp/UDLPM26cBc/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/UDLPM26cBc/merge.gvcf.10.b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/UDLPM26cBc/merge.gvcf.10.b.vcf.gz /tmp/UDLPM26cBc/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/UDLPM26cBc/merge.gvcf.10.b.bcf /tmp/UDLPM26cBc/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/UDLPM26cBc/merge.gvcf.10.b.bcf /tmp/UDLPM26cBc/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/UDLPM26cBc/merge.noidx.a.vcf.gz /tmp/UDLPM26cBc/merge.noidx.b.vcf.gz /tmp/UDLPM26cBc/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/UDLPM26cBc/merge.noidx.a.vcf.gz /tmp/UDLPM26cBc/merge.noidx.b.vcf.gz /tmp/UDLPM26cBc/merge.noidx.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/UDLPM26cBc/merge.noidx.a.bcf /tmp/UDLPM26cBc/merge.noidx.b.bcf /tmp/UDLPM26cBc/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/UDLPM26cBc/merge.noidx.a.bcf /tmp/UDLPM26cBc/merge.noidx.b.bcf /tmp/UDLPM26cBc/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --no-index /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.c.vcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --no-index /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.c.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --no-index /tmp/UDLPM26cBc/merge.noidx.a.bcf /tmp/UDLPM26cBc/merge.noidx.b.bcf /tmp/UDLPM26cBc/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --no-index /tmp/UDLPM26cBc/merge.noidx.a.bcf /tmp/UDLPM26cBc/merge.noidx.b.bcf /tmp/UDLPM26cBc/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/UDLPM26cBc/merge.8.a.vcf.gz /tmp/UDLPM26cBc/merge.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/UDLPM26cBc/merge.8.a.vcf.gz /tmp/UDLPM26cBc/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/UDLPM26cBc/merge.8.a.bcf /tmp/UDLPM26cBc/merge.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/UDLPM26cBc/merge.8.a.bcf /tmp/UDLPM26cBc/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/UDLPM26cBc/merge.8.a.vcf.gz /tmp/UDLPM26cBc/merge.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/UDLPM26cBc/merge.8.a.vcf.gz /tmp/UDLPM26cBc/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/UDLPM26cBc/merge.8.a.bcf /tmp/UDLPM26cBc/merge.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/UDLPM26cBc/merge.8.a.bcf /tmp/UDLPM26cBc/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/UDLPM26cBc/merge.9.a.vcf.gz /tmp/UDLPM26cBc/merge.9.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/UDLPM26cBc/merge.9.a.vcf.gz /tmp/UDLPM26cBc/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/UDLPM26cBc/merge.9.a.bcf /tmp/UDLPM26cBc/merge.9.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/UDLPM26cBc/merge.9.a.bcf /tmp/UDLPM26cBc/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/UDLPM26cBc/merge.9.a.vcf.gz /tmp/UDLPM26cBc/merge.9.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/UDLPM26cBc/merge.9.a.vcf.gz /tmp/UDLPM26cBc/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/UDLPM26cBc/merge.9.a.bcf /tmp/UDLPM26cBc/merge.9.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/UDLPM26cBc/merge.9.a.bcf /tmp/UDLPM26cBc/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/UDLPM26cBc/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/UDLPM26cBc/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/UDLPM26cBc/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%RSX\t%VKX\n' /tmp/UDLPM26cBc/query.variantkey.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.variantkey.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/UDLPM26cBc/view.vectors.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/UDLPM26cBc/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/UDLPM26cBc/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/UDLPM26cBc/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/UDLPM26cBc/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/UDLPM26cBc/query.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/UDLPM26cBc/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/UDLPM26cBc/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/UDLPM26cBc/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/UDLPM26cBc/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%LINE' /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%LINE' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/UDLPM26cBc/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/UDLPM26cBc/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/UDLPM26cBc/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/UDLPM26cBc/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/UDLPM26cBc/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/UDLPM26cBc/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/UDLPM26cBc/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/UDLPM26cBc/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/UDLPM26cBc/query.filter.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/UDLPM26cBc/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/UDLPM26cBc/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/UDLPM26cBc/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/UDLPM26cBc/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/UDLPM26cBc/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/UDLPM26cBc/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/UDLPM26cBc/query.filter.4.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.56.out' /tmp/UDLPM26cBc/view.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.56.out' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/UDLPM26cBc/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/UDLPM26cBc/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/UDLPM26cBc/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/UDLPM26cBc/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/UDLPM26cBc/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/UDLPM26cBc/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/UDLPM26cBc/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/UDLPM26cBc/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/UDLPM26cBc/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/UDLPM26cBc/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/UDLPM26cBc/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' /tmp/UDLPM26cBc/query.pbinom.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.pbinom.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/UDLPM26cBc/query.filter.6.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.6.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/UDLPM26cBc/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/UDLPM26cBc/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/UDLPM26cBc/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/UDLPM26cBc/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/UDLPM26cBc/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/UDLPM26cBc/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/UDLPM26cBc/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/UDLPM26cBc/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/UDLPM26cBc/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/UDLPM26cBc/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/UDLPM26cBc/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/UDLPM26cBc/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/UDLPM26cBc/query.filter.13.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.13.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/UDLPM26cBc/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/UDLPM26cBc/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/UDLPM26cBc/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/UDLPM26cBc/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/UDLPM26cBc/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt /tmp/UDLPM26cBc/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt /tmp/UDLPM26cBc/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt /tmp/UDLPM26cBc/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt /tmp/UDLPM26cBc/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.txt /tmp/UDLPM26cBc/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.txt /tmp/UDLPM26cBc/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/UDLPM26cBc/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/UDLPM26cBc/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -cx -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/UDLPM26cBc/norm.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -cx -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/UDLPM26cBc/norm.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/UDLPM26cBc/norm.split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/UDLPM26cBc/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/UDLPM26cBc/norm.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/UDLPM26cBc/norm.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- --force /tmp/UDLPM26cBc/norm.split.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- --force /tmp/UDLPM26cBc/norm.split.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/UDLPM26cBc/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/UDLPM26cBc/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- --keep-sum AD /tmp/UDLPM26cBc/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- --keep-sum AD /tmp/UDLPM26cBc/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/UDLPM26cBc/norm.split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/UDLPM26cBc/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/UDLPM26cBc/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/UDLPM26cBc/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/UDLPM26cBc/norm.merge.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/UDLPM26cBc/norm.merge.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/UDLPM26cBc/norm.merge.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/UDLPM26cBc/norm.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m+ -s /tmp/UDLPM26cBc/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m+ -s /tmp/UDLPM26cBc/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -Nc s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/UDLPM26cBc/norm.setref.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -Nc s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/UDLPM26cBc/norm.setref.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/UDLPM26cBc/norm.telomere.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/UDLPM26cBc/norm.telomere.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d snps /tmp/UDLPM26cBc/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d snps /tmp/UDLPM26cBc/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d indels /tmp/UDLPM26cBc/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d indels /tmp/UDLPM26cBc/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d both /tmp/UDLPM26cBc/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d both /tmp/UDLPM26cBc/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d all /tmp/UDLPM26cBc/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d all /tmp/UDLPM26cBc/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d none /tmp/UDLPM26cBc/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d none /tmp/UDLPM26cBc/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d exact /tmp/UDLPM26cBc/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d exact /tmp/UDLPM26cBc/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d none /tmp/UDLPM26cBc/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d none /tmp/UDLPM26cBc/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d exact /tmp/UDLPM26cBc/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d exact /tmp/UDLPM26cBc/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d indels /tmp/UDLPM26cBc/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d indels /tmp/UDLPM26cBc/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d any /tmp/UDLPM26cBc/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d any /tmp/UDLPM26cBc/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d both /tmp/UDLPM26cBc/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d both /tmp/UDLPM26cBc/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d snps /tmp/UDLPM26cBc/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d snps /tmp/UDLPM26cBc/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -c s -a -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.2.fa /tmp/UDLPM26cBc/norm.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -c s -a -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.2.fa /tmp/UDLPM26cBc/norm.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -c s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.iupac.fa /tmp/UDLPM26cBc/norm.iupac.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -c s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.iupac.fa /tmp/UDLPM26cBc/norm.iupac.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -c s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.3.fa /tmp/UDLPM26cBc/norm.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -c s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.3.fa /tmp/UDLPM26cBc/norm.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/UDLPM26cBc/atomize.split.1.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/UDLPM26cBc/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/UDLPM26cBc/atomize.split.1.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/UDLPM26cBc/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/UDLPM26cBc/atomize.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/UDLPM26cBc/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/UDLPM26cBc/atomize.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/UDLPM26cBc/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . /tmp/UDLPM26cBc/atomize.split.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . /tmp/UDLPM26cBc/atomize.split.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m +both /tmp/UDLPM26cBc/norm.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m +both /tmp/UDLPM26cBc/norm.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m +any /tmp/UDLPM26cBc/norm.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m +any /tmp/UDLPM26cBc/norm.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/UDLPM26cBc/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/UDLPM26cBc/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -f PASS -Xks NA00003 /tmp/UDLPM26cBc/view.vcf.gz -r20,Y .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -f PASS -Xks NA00003 /tmp/UDLPM26cBc/view.vcf.gz -r20,Y | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -xs NA00003 /tmp/UDLPM26cBc/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -xs NA00003 /tmp/UDLPM26cBc/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/UDLPM26cBc/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/UDLPM26cBc/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -p /tmp/UDLPM26cBc/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -p /tmp/UDLPM26cBc/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -P /tmp/UDLPM26cBc/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -P /tmp/UDLPM26cBc/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/UDLPM26cBc/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/UDLPM26cBc/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -Hu /tmp/UDLPM26cBc/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -GVsnps /tmp/UDLPM26cBc/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -GVsnps /tmp/UDLPM26cBc/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/UDLPM26cBc/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/UDLPM26cBc/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -s ^NA00003 /tmp/UDLPM26cBc/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -s ^NA00003 /tmp/UDLPM26cBc/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version /tmp/UDLPM26cBc/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -G /tmp/UDLPM26cBc/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -G /tmp/UDLPM26cBc/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -HG /tmp/UDLPM26cBc/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -a /tmp/UDLPM26cBc/many.alleles.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -a /tmp/UDLPM26cBc/many.alleles.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -asA /tmp/UDLPM26cBc/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -asA /tmp/UDLPM26cBc/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -asB /tmp/UDLPM26cBc/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -asB /tmp/UDLPM26cBc/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -asA /tmp/UDLPM26cBc/view.vectors.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -asA /tmp/UDLPM26cBc/view.vectors.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'TXT0="text"' /tmp/UDLPM26cBc/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.chrs.tab /tmp/UDLPM26cBc/view.chrs.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.chrs.tab /tmp/UDLPM26cBc/view.chrs.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -i 'POS>=3062917' /tmp/UDLPM26cBc/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -i 'POS>=3062917' /tmp/UDLPM26cBc/filter.2.vcf.gz 1:3062917-3157410 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/UDLPM26cBc/idx.1.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/UDLPM26cBc/idx.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/idx.2.bed /tmp/UDLPM26cBc/idx.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/idx.3.bed /tmp/UDLPM26cBc/idx.3.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/idx.4.bed /tmp/UDLPM26cBc/idx.4.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -Ht 2 /tmp/UDLPM26cBc/view-t.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -Ht 3 /tmp/UDLPM26cBc/view-t.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/UDLPM26cBc/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/UDLPM26cBc/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/UDLPM26cBc/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/UDLPM26cBc/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/UDLPM26cBc/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/UDLPM26cBc/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/UDLPM26cBc/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/UDLPM26cBc/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/UDLPM26cBc/overlap.vcf.gz .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.1.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.2.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.4.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.5.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -C5:nonmajor /tmp/UDLPM26cBc/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -c6:nonmajor /tmp/UDLPM26cBc/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -q0.3:major /tmp/UDLPM26cBc/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/UDLPM26cBc/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/UDLPM26cBc/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/UDLPM26cBc/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -a /tmp/UDLPM26cBc/view-a.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.sites.txt /tmp/UDLPM26cBc/view.sites.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.sites.txt /tmp/UDLPM26cBc/view.sites.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.sites.txt.gz /tmp/UDLPM26cBc/view.sites.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.sites.txt.gz /tmp/UDLPM26cBc/view.sites.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 5 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 22 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 23 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -n 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -n 1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -n 5 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 5 -n 5 < /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mg0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mg0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.cals.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/UDLPM26cBc/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.cals.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -cv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -cv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.2.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'ALT="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'ALT="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="A"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="A"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="RR"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="RR"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="RA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="RA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="AR"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="AR"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="AA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="AA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="aA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="aA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="HET"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="HET"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.7.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools sort -m 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools sort -Ob -m 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools sort -m 1000 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools sort -Ob -m 1000 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/regions.tab /tmp/UDLPM26cBc/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/regions.tab .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/regions.tab /tmp/UDLPM26cBc/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/UDLPM26cBc/regions.tab.gz /tmp/UDLPM26cBc/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/UDLPM26cBc/regions.tab.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/UDLPM26cBc/regions.tab.gz /tmp/UDLPM26cBc/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/UDLPM26cBc/regions.bed /tmp/UDLPM26cBc/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/UDLPM26cBc/regions.bed .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/UDLPM26cBc/regions.bed /tmp/UDLPM26cBc/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/UDLPM26cBc/regions.bed.gz /tmp/UDLPM26cBc/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/UDLPM26cBc/regions.bed.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/UDLPM26cBc/regions.bed.gz /tmp/UDLPM26cBc/regions.vcf.gz .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/UDLPM26cBc/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/UDLPM26cBc/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -x FORMAT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -x FORMAT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots4.vcf.gz -c +INFO /tmp/UDLPM26cBc/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots4.vcf.gz -c +INFO /tmp/UDLPM26cBc/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots11.vcf.gz -c FMT /tmp/UDLPM26cBc/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots11.vcf.gz -c FMT /tmp/UDLPM26cBc/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots2.vcf.gz -c FMT/newGT:=GT /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots2.vcf.gz -c FMT/newGT:=GT /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots12.vcf.gz -c FMT/GT:=newGT /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots12.vcf.gz -c FMT/GT:=newGT /tmp/UDLPM26cBc/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -x FILTER /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -x FILTER /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/UDLPM26cBc/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/UDLPM26cBc/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/UDLPM26cBc/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/UDLPM26cBc/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate20.src.vcf.gz -c FMT/GT /tmp/UDLPM26cBc/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate20.src.vcf.gz -c FMT/GT /tmp/UDLPM26cBc/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate20.src.vcf.gz -c +FMT/GT /tmp/UDLPM26cBc/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate20.src.vcf.gz -c +FMT/GT /tmp/UDLPM26cBc/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate20.src.vcf.gz -c -FMT/GT /tmp/UDLPM26cBc/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate20.src.vcf.gz -c -FMT/GT /tmp/UDLPM26cBc/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-annots /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.txt /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob --rename-annots /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.txt /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/UDLPM26cBc/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/UDLPM26cBc/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate24.src.vcf.gz -c XX /tmp/UDLPM26cBc/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate24.src.vcf.gz -c XX /tmp/UDLPM26cBc/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate26.tab.gz -c CHROM,POS,~POS /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate26.tab.gz -c CHROM,POS,~POS /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots.id.vcf.gz -c ALT /tmp/UDLPM26cBc/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots.id.vcf.gz -c ALT /tmp/UDLPM26cBc/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/UDLPM26cBc/annots.id.vcf.gz -c +ALT /tmp/UDLPM26cBc/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/UDLPM26cBc/annots.id.vcf.gz -c +ALT /tmp/UDLPM26cBc/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/UDLPM26cBc/checkploidy.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/UDLPM26cBc/checkploidy.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/UDLPM26cBc/checkploidy.2.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/UDLPM26cBc/checkploidy.2.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/UDLPM26cBc/checkploidy.2.vcf.gz -- -m | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/UDLPM26cBc/checkploidy.2.bcf -- -m | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +missing2ref --no-version /tmp/UDLPM26cBc/plugin1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +missing2ref --no-version /tmp/UDLPM26cBc/plugin1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/plugin1.vcf.gz -- -t . -n 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/plugin1.bcf -- -t . -n 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.3.vcf.gz -- -t a -n pM | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.3.bcf -- -t a -n pM | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.3.vcf.gz -- -t a -n pm | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.3.bcf -- -t a -n pm | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.3.vcf.gz -- -t a -n c:1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.3.bcf -- -t a -n c:1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.3.vcf.gz -- -t a -n c:"1|1" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.3.bcf -- -t a -n c:"1|1" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.3.vcf.gz -- -t a -n c:"m|M" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.3.bcf -- -t a -n c:"m|M" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.3.vcf.gz -- -t a -n c:0/1/1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.3.bcf -- -t a -n c:0/1/1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.4.bcf -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/UDLPM26cBc/setGT.4.bcf -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-AN-AC --no-version /tmp/UDLPM26cBc/plugin1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-AN-AC --no-version /tmp/UDLPM26cBc/plugin1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/UDLPM26cBc/dosage.vcf.gz -- -t PL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/UDLPM26cBc/dosage.bcf -- -t PL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/UDLPM26cBc/dosage.vcf.gz -- -t GL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/UDLPM26cBc/dosage.bcf -- -t GL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/UDLPM26cBc/dosage.vcf.gz -- -t GT | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/UDLPM26cBc/dosage.bcf -- -t GT | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixploidy --no-version /tmp/UDLPM26cBc/fixploidy.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixploidy.ploidy | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixploidy --no-version /tmp/UDLPM26cBc/fixploidy.bcf -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixploidy.ploidy | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +guess-ploidy /tmp/UDLPM26cBc/view.PL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +guess-ploidy /tmp/UDLPM26cBc/view.PL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +guess-ploidy /tmp/UDLPM26cBc/view.GL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +guess-ploidy /tmp/UDLPM26cBc/view.GL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/UDLPM26cBc/view.GL.vcf.gz -- -r --gl-to-pl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/UDLPM26cBc/view.GL.bcf -- -r --gl-to-pl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/UDLPM26cBc/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/UDLPM26cBc/view.GP.bcf -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +add-variantkey /tmp/UDLPM26cBc/query.variantkey.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +add-variantkey /tmp/UDLPM26cBc/query.variantkey.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +variantkey-hex /tmp/UDLPM26cBc/query.variantkey.vcf.gz test/ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +variantkey-hex /tmp/UDLPM26cBc/query.variantkey.bcf test/ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +allele-length /tmp/UDLPM26cBc/query.nucleotide.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +allele-length /tmp/UDLPM26cBc/query.nucleotide.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/view.vcf.gz -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/view.bcf -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/view.vcf.gz -- -t AC -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/view.bcf -- -t AC -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/view.vcf.gz -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/view.bcf -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/many-alts.vcf.gz -- -t AN,AC | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/many-alts.bcf -- -t AN,AC | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-hemi.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-hemi.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-hemi.vcf.gz -- -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-hemi.bcf -- -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-hwe.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-hwe.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-hwe.vcf.gz -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-hwe.bcf -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-AN0.vcf.gz -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-AN0.bcf -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-VAF.vcf.gz -- -t VAF,VAF1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-VAF.bcf -- -t VAF,VAF1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-AD.vcf.gz -- -t 'FORMAT/DP:1=int(smpl_sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-AD.bcf -- -t 'FORMAT/DP:1=int(smpl_sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-AD.vcf.gz -- -t 'XX=N_PASS(FMT/AD[:0]<=10)','YY=N_PASS(FMT/AD[:0]>10)' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/UDLPM26cBc/fill-tags-AD.bcf -- -t 'XX=N_PASS(FMT/AD[:0]<=10)','YY=N_PASS(FMT/AD[:0]>10)' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.vcf.gz | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.bcf | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.vcf.gz -- -H | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.bcf -- -H | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.vcf.gz -- -Hm | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.bcf -- -Hm | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.vcf.gz -- -Hmv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.bcf -- -Hmv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.vcf.gz -- -Hv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.bcf -- -Hv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.vcf.gz -- -m | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.bcf -- -m | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.vcf.gz -- -mv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.bcf -- -mv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.vcf.gz -- -v | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/UDLPM26cBc/view.bcf -- -v | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-switch-rate /tmp/UDLPM26cBc/trio.vcf.gz -- -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-switch-rate /tmp/UDLPM26cBc/trio.bcf -- -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-stats /tmp/UDLPM26cBc/trio-stats.vcf.gz -a 1 -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-stats /tmp/UDLPM26cBc/trio-stats.bcf -a 1 -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-stats /tmp/UDLPM26cBc/trio-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-stats /tmp/UDLPM26cBc/trio-stats.bcf -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +smpl-stats /tmp/UDLPM26cBc/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +smpl-stats /tmp/UDLPM26cBc/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/UDLPM26cBc/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/UDLPM26cBc/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/UDLPM26cBc/indel-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/UDLPM26cBc/indel-stats.bcf -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/UDLPM26cBc/indel-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/UDLPM26cBc/indel-stats.bcf -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/UDLPM26cBc/ad-bias.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/UDLPM26cBc/ad-bias.bcf -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/UDLPM26cBc/ad-bias.2.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/UDLPM26cBc/ad-bias.2.bcf -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/UDLPM26cBc/ad-bias.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/UDLPM26cBc/ad-bias.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/UDLPM26cBc/ad-bias.2.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/UDLPM26cBc/ad-bias.2.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +af-dist /tmp/UDLPM26cBc/af-dist.vcf.gz | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +af-dist /tmp/UDLPM26cBc/af-dist.bcf | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/UDLPM26cBc/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -i /tmp/UDLPM26cBc/fixref.2b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/UDLPM26cBc/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -i /tmp/UDLPM26cBc/fixref.2b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/UDLPM26cBc/fixref.3.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixref.3.fa -m top | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/UDLPM26cBc/fixref.3.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixref.3.fa -m top | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/UDLPM26cBc/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m ref-alt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/UDLPM26cBc/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m ref-alt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/UDLPM26cBc/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m flip | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/UDLPM26cBc/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m flip | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/UDLPM26cBc/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m flip-all | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/UDLPM26cBc/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m flip-all | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/UDLPM26cBc/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/UDLPM26cBc/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/UDLPM26cBc/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.fa -c REF -N | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/UDLPM26cBc/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.fa -c REF -N | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/UDLPM26cBc/ref.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -c REF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/UDLPM26cBc/ref.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -c REF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/UDLPM26cBc/view.vcf.gz -- -s NA00001 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/UDLPM26cBc/view.bcf -- -s NA00001 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/UDLPM26cBc/view.vcf.gz -- -s NA00001,NA00002 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/UDLPM26cBc/view.bcf -- -s NA00001,NA00002 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/UDLPM26cBc/view.vcf.gz -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/UDLPM26cBc/view.bcf -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/UDLPM26cBc/mendelian.vcf.gz -t mom1,dad1,child1 -md | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/UDLPM26cBc/mendelian.bcf -t mom1,dad1,child1 -md | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/UDLPM26cBc/mendelian.vcf.gz -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/UDLPM26cBc/mendelian.bcf -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/UDLPM26cBc/mendelian.vcf.gz -t mom1,dad1,child1 -mx | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/UDLPM26cBc/mendelian.bcf -t mom1,dad1,child1 -mx | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/UDLPM26cBc/mendelian.vcf.gz -t mom1,dad1,child1 -ma | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/UDLPM26cBc/mendelian.bcf -t mom1,dad1,child1 -ma | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/UDLPM26cBc/mendelian.vcf.gz -t mom1,dad1,child1 -mu | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/UDLPM26cBc/mendelian.bcf -t mom1,dad1,child1 -mu | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/UDLPM26cBc/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/UDLPM26cBc/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/UDLPM26cBc/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/contrast1.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/UDLPM26cBc/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/contrast1.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/UDLPM26cBc/contrast.vcf.gz -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/UDLPM26cBc/contrast.bcf -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/UDLPM26cBc/contrast.1.vcf.gz -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/UDLPM26cBc/contrast.1.bcf -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/UDLPM26cBc/contrast.1.vcf.gz -a NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/UDLPM26cBc/contrast.1.bcf -a NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.1.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.1.bcf -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.2.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.2.bcf -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.4.bcf -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.8.vcf.gz -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.8.bcf -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.9.vcf.gz -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.9.bcf -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.9.vcf.gz -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.9.bcf -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.10.vcf.gz -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/UDLPM26cBc/trio-dnm/trio-dnm.10.bcf -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/UDLPM26cBc/gvcfz.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/UDLPM26cBc/gvcfz.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/UDLPM26cBc/gvcfz.vcf.gz -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/UDLPM26cBc/gvcfz.bcf -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/UDLPM26cBc/gvcfz.2.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/UDLPM26cBc/gvcfz.2.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +remove-overlaps /tmp/UDLPM26cBc/remove-overlaps.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +remove-overlaps /tmp/UDLPM26cBc/remove-overlaps.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +remove-overlaps /tmp/UDLPM26cBc/remove-overlaps.vcf.gz -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +remove-overlaps /tmp/UDLPM26cBc/remove-overlaps.bcf -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.vcf.gz -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.bcf -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.vcf.gz -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.bcf -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.vcf.gz -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.bcf -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.2.vcf.gz -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.2.bcf -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.2.vcf.gz -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.2.bcf -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.3.vcf.gz -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.3.bcf -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.3.vcf.gz -s worst -f'[%POS\t%SAMPLE\t%GT\t%Consequence\n]' -i'GT="alt"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.3.bcf -s worst -f'[%POS\t%SAMPLE\t%GT\t%Consequence\n]' -i'GT="alt"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.4.bcf -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.vcf.gz -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.bcf -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.vcf.gz -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.bcf -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.5.vcf.gz -s :synonymous -c Consequence | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.5.bcf -s :synonymous -c Consequence | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.5.vcf.gz -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.5.bcf -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.6.vcf.gz -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.6.bcf -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.6.vcf.gz -c - | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.6.bcf -c - | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.6.vcf.gz -c - -s worst | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.6.bcf -c - -s worst | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.7.vcf.gz --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.7.bcf --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.8.vcf.gz -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.8.bcf -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.8.vcf.gz -a BCSQ -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.8.bcf -a BCSQ -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.9.vcf.gz -a BCSQ -f '%CHROM\t%POS\t%REF\t%ALT\t%BCSQ\n' -d -A tab | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.9.bcf -a BCSQ -f '%CHROM\t%POS\t%REF\t%ALT\t%BCSQ\n' -d -A tab | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.9.vcf.gz -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.9.bcf -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.10.vcf.gz -a CSQ -f '%M_CAP_pred %M_CAP_score\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.10.bcf -a CSQ -f '%M_CAP_pred %M_CAP_score\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.10.vcf.gz -a CSQ -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/UDLPM26cBc/split-vep.10.bcf -a CSQ -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/UDLPM26cBc/parental-origin.vcf.gz -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/UDLPM26cBc/parental-origin.bcf -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/UDLPM26cBc/parental-origin.vcf.gz -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/UDLPM26cBc/parental-origin.bcf -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/UDLPM26cBc/parental-origin.vcf.gz -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/UDLPM26cBc/parental-origin.bcf -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/UDLPM26cBc/parental-origin.vcf.gz -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/UDLPM26cBc/parental-origin.bcf -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/UDLPM26cBc/parental-origin.vcf.gz -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/UDLPM26cBc/parental-origin.bcf -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/UDLPM26cBc/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/UDLPM26cBc/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/UDLPM26cBc/prune.2.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/UDLPM26cBc/prune.2.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/UDLPM26cBc/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/UDLPM26cBc/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/UDLPM26cBc/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/UDLPM26cBc/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/UDLPM26cBc/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/UDLPM26cBc/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/UDLPM26cBc/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/UDLPM26cBc/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N 1st /tmp/UDLPM26cBc/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N 1st /tmp/UDLPM26cBc/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/UDLPM26cBc/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/UDLPM26cBc/prune.1.bcf | grep -v ^##bcftools_ .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/UDLPM26cBc/split.1.1 && cd /tmp/UDLPM26cBc/split.1.1 && for f in A1.vcf A2.vcf A3.vcf B1.vcf B2.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/UDLPM26cBc/split.1.2 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.2.txt && cd /tmp/UDLPM26cBc/split.1.2 && for f in A.vcf B.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/UDLPM26cBc/split.1.3 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.3.txt && cd /tmp/UDLPM26cBc/split.1.3 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/UDLPM26cBc/split.1.4 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.3.txt -i 'GT[0]="alt"' && cd /tmp/UDLPM26cBc/split.1.4 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/UDLPM26cBc/split.1.5 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.3.txt -i 'GT="alt"' && cd /tmp/UDLPM26cBc/split.1.5 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/UDLPM26cBc/split.1.6 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.4.txt -i 'GT="alt"' && cd /tmp/UDLPM26cBc/split.1.6 && for f in file1.vcf file2.vcf file3.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/UDLPM26cBc/split.1.7 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.grp.1.1.txt && cd /tmp/UDLPM26cBc/split.1.7 && for f in A.vcf A1.vcf A2.vcf B.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.2.vcf -o /tmp/UDLPM26cBc/split.2.1 && cd /tmp/UDLPM26cBc/split.2.1 && for f in A1_A1-1.vcf A1_A1-2.vcf A1_A1.vcf B1.vcf B2.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/UDLPM26cBc/scatter.1.1 -n 3 && cd /tmp/UDLPM26cBc/scatter.1.1 && cat 0.vcf 1.vcf 2.vcf | grep -v ^## .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/UDLPM26cBc/scatter.1.2 -s 21,22 && cd /tmp/UDLPM26cBc/scatter.1.2 && cat 21.vcf 22.vcf | grep -v ^## .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/UDLPM26cBc/scatter.1.3 -s 21,22 -x X && cd /tmp/UDLPM26cBc/scatter.1.3 && cat 21.vcf 22.vcf X.vcf | grep -v ^## .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version /tmp/UDLPM26cBc/concat.1.a.vcf.gz /tmp/UDLPM26cBc/concat.1.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob /tmp/UDLPM26cBc/concat.1.a.vcf.gz /tmp/UDLPM26cBc/concat.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version /tmp/UDLPM26cBc/concat.1.a.bcf /tmp/UDLPM26cBc/concat.1.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob /tmp/UDLPM26cBc/concat.1.a.bcf /tmp/UDLPM26cBc/concat.1.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -a /tmp/UDLPM26cBc/concat.2.a.vcf.gz /tmp/UDLPM26cBc/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -a /tmp/UDLPM26cBc/concat.2.a.vcf.gz /tmp/UDLPM26cBc/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -a /tmp/UDLPM26cBc/concat.2.a.bcf /tmp/UDLPM26cBc/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -a /tmp/UDLPM26cBc/concat.2.a.bcf /tmp/UDLPM26cBc/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -aD /tmp/UDLPM26cBc/concat.2.a.vcf.gz /tmp/UDLPM26cBc/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -aD /tmp/UDLPM26cBc/concat.2.a.vcf.gz /tmp/UDLPM26cBc/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -aD /tmp/UDLPM26cBc/concat.2.a.bcf /tmp/UDLPM26cBc/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -aD /tmp/UDLPM26cBc/concat.2.a.bcf /tmp/UDLPM26cBc/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/UDLPM26cBc/concat.3.a.vcf.gz /tmp/UDLPM26cBc/concat.3.b.vcf.gz /tmp/UDLPM26cBc/concat.3.0.vcf.gz /tmp/UDLPM26cBc/concat.3.c.vcf.gz /tmp/UDLPM26cBc/concat.3.d.vcf.gz /tmp/UDLPM26cBc/concat.3.e.vcf.gz /tmp/UDLPM26cBc/concat.3.f.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/UDLPM26cBc/concat.3.a.vcf.gz /tmp/UDLPM26cBc/concat.3.b.vcf.gz /tmp/UDLPM26cBc/concat.3.0.vcf.gz /tmp/UDLPM26cBc/concat.3.c.vcf.gz /tmp/UDLPM26cBc/concat.3.d.vcf.gz /tmp/UDLPM26cBc/concat.3.e.vcf.gz /tmp/UDLPM26cBc/concat.3.f.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/UDLPM26cBc/concat.3.a.bcf /tmp/UDLPM26cBc/concat.3.b.bcf /tmp/UDLPM26cBc/concat.3.0.bcf /tmp/UDLPM26cBc/concat.3.c.bcf /tmp/UDLPM26cBc/concat.3.d.bcf /tmp/UDLPM26cBc/concat.3.e.bcf /tmp/UDLPM26cBc/concat.3.f.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/UDLPM26cBc/concat.3.a.bcf /tmp/UDLPM26cBc/concat.3.b.bcf /tmp/UDLPM26cBc/concat.3.0.bcf /tmp/UDLPM26cBc/concat.3.c.bcf /tmp/UDLPM26cBc/concat.3.d.bcf /tmp/UDLPM26cBc/concat.3.e.bcf /tmp/UDLPM26cBc/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 3379579982 .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --naive-force /tmp/UDLPM26cBc/naive_concat.0.bcf /tmp/UDLPM26cBc/naive_concat.1.bcf /tmp/UDLPM26cBc/naive_concat.2.bcf /tmp/UDLPM26cBc/naive_concat.3.bcf /tmp/UDLPM26cBc/naive_concat.4.bcf /tmp/UDLPM26cBc/naive_concat.5.bcf /tmp/UDLPM26cBc/naive_concat.6.bcf /tmp/UDLPM26cBc/naive_concat.7.bcf /tmp/UDLPM26cBc/naive_concat.8.bcf /tmp/UDLPM26cBc/naive_concat.9.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --naive /tmp/UDLPM26cBc/naive_concat.0.vcf.gz /tmp/UDLPM26cBc/naive_concat.1.vcf.gz /tmp/UDLPM26cBc/naive_concat.2.vcf.gz /tmp/UDLPM26cBc/naive_concat.3.vcf.gz /tmp/UDLPM26cBc/naive_concat.4.vcf.gz /tmp/UDLPM26cBc/naive_concat.5.vcf.gz /tmp/UDLPM26cBc/naive_concat.6.vcf.gz /tmp/UDLPM26cBc/naive_concat.7.vcf.gz /tmp/UDLPM26cBc/naive_concat.8.vcf.gz /tmp/UDLPM26cBc/naive_concat.9.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l /tmp/UDLPM26cBc/concat.4.a.vcf.gz /tmp/UDLPM26cBc/concat.4.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l /tmp/UDLPM26cBc/concat.4.a.vcf.gz /tmp/UDLPM26cBc/concat.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l /tmp/UDLPM26cBc/concat.4.a.bcf /tmp/UDLPM26cBc/concat.4.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l /tmp/UDLPM26cBc/concat.4.a.bcf /tmp/UDLPM26cBc/concat.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/UDLPM26cBc/concat.5.a.vcf.gz /tmp/UDLPM26cBc/concat.5.b.vcf.gz /tmp/UDLPM26cBc/concat.5.c.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/UDLPM26cBc/concat.5.a.vcf.gz /tmp/UDLPM26cBc/concat.5.b.vcf.gz /tmp/UDLPM26cBc/concat.5.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/UDLPM26cBc/concat.5.a.bcf /tmp/UDLPM26cBc/concat.5.b.bcf /tmp/UDLPM26cBc/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/UDLPM26cBc/concat.5.a.bcf /tmp/UDLPM26cBc/concat.5.b.bcf /tmp/UDLPM26cBc/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-force /tmp/UDLPM26cBc/concat.5.a.bcf /tmp/UDLPM26cBc/concat.5.b.bcf /tmp/UDLPM26cBc/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-force /tmp/UDLPM26cBc/concat.5.a.bcf /tmp/UDLPM26cBc/concat.5.b.bcf /tmp/UDLPM26cBc/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr /tmp/UDLPM26cBc/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UDLPM26cBc/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr /tmp/UDLPM26cBc/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UDLPM26cBc/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples /tmp/UDLPM26cBc/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UDLPM26cBc/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples /tmp/UDLPM26cBc/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UDLPM26cBc/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 /tmp/UDLPM26cBc/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UDLPM26cBc/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 /tmp/UDLPM26cBc/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UDLPM26cBc/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 /tmp/UDLPM26cBc/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UDLPM26cBc/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 /tmp/UDLPM26cBc/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UDLPM26cBc/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 /tmp/UDLPM26cBc/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UDLPM26cBc/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 /tmp/UDLPM26cBc/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UDLPM26cBc/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/empty.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/empty.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr /tmp/UDLPM26cBc/empty.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UDLPM26cBc/empty.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr /tmp/UDLPM26cBc/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UDLPM26cBc/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /tmp/UDLPM26cBc/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /tmp/UDLPM26cBc/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /tmp/UDLPM26cBc/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /tmp/UDLPM26cBc/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/UDLPM26cBc/rename.map -Ov /tmp/UDLPM26cBc/annotate.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/UDLPM26cBc/rename.map -Ob /tmp/UDLPM26cBc/annotate.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/UDLPM26cBc/rename.map -Ov /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/UDLPM26cBc/rename.map -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. /tmp/UDLPM26cBc/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids /tmp/UDLPM26cBc/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids --3N6 /tmp/UDLPM26cBc/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- /tmp/UDLPM26cBc/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --tag PL /tmp/UDLPM26cBc/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --tag PL /tmp/UDLPM26cBc/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids /tmp/UDLPM26cBc/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --vcf-ids /tmp/UDLPM26cBc/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --3N6 /tmp/UDLPM26cBc/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --3N6 /tmp/UDLPM26cBc/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --3N6 --vcf-ids /tmp/UDLPM26cBc/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --3N6 --vcf-ids /tmp/UDLPM26cBc/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h -,.,. /tmp/UDLPM26cBc/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h -,.,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,-,. /tmp/UDLPM26cBc/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,-,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,-,. --vcf-ids /tmp/UDLPM26cBc/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,.,- /tmp/UDLPM26cBc/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -H /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -H /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --haplegendsample -,.,. /tmp/UDLPM26cBc/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.hap-missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample -,. /tmp/UDLPM26cBc/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample -,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample -,. --vcf-ids /tmp/UDLPM26cBc/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample .,- /tmp/UDLPM26cBc/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/UDLPM26cBc/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/UDLPM26cBc/convert.gvcf.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.23andme | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab -c /tmp/UDLPM26cBc/consensus.1.chain.new >/dev/null; cat /tmp/UDLPM26cBc/consensus.1.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab -c /tmp/UDLPM26cBc/consensus.2.chain.new >/dev/null; cat /tmp/UDLPM26cBc/consensus.2.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab --mask-with X -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab -c /tmp/UDLPM26cBc/consensus.3.chain.new >/dev/null; cat /tmp/UDLPM26cBc/consensus.3.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H 1 -c /tmp/UDLPM26cBc/consensus.4.chain.new >/dev/null; cat /tmp/UDLPM26cBc/consensus.4.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/empty.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus4.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus5.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus6.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus6.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . -i 'ALT!=""' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . -e 'MinDP>15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . -e 'MinDP<15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.12.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.13.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.13.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.14.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.14.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.12.fa --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.15.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -I .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H I .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.17.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -M N -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.17.bed .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.18.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.18.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/UDLPM26cBc/consensus.19.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.19.fa .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -b /tmp/UDLPM26cBc/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob -b /tmp/UDLPM26cBc/mpileup.bam.urllist | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -b /tmp/UDLPM26cBc/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob -b /tmp/UDLPM26cBc/mpileup.cram.urllist | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.gff3 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.chr.gff3 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.2.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.2.gff --ncsq 64 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0002/EDUMMY0002.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0002/EDUMMY0002.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0002/boundaries.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0003/EDUMMY0003.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0003/EDUMMY0003.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0003/long-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSG00000173376/ENSG00000173376.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSG00000173376/ENSG00000173376.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSG00000173376/synon.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSMUST00000133836 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000000000 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/start-lost-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000227471/ENST00000227471.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000227471/ENST00000227471.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000230048/ENST00000230048.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000230048/ENST00000230048.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000230048/start-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000256452/ENST00000256452.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000256452/ENST00000256452.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000256452/intron.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000263103-INS/insertions.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000269081/ENST00000269081.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000269081/ENST00000269081.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000271583/ENST00000271583.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000271583/ENST00000271583.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000271583/splice-acceptor.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000285021/ENST00000285021.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000285021/ENST00000285021.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000301246/ENST00000301246.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000301246/ENST00000301246.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000301246/15bp-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249.2/ENST00000318249.2.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000357367/ENST00000357367.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000357367/ENST00000357367.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000357367/stop-retained.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801.2/ENST00000368801.2.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801.2/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801/ENST00000368801.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801/ENST00000368801.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801/compound-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000375992/ENST00000375992.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000375992/ENST00000375992.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000379416 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000381157/ENST00000381157.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000381157/ENST00000381157.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000381157/haploid-diploid.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000382647/ENST00000382647.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000382647/ENST00000382647.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000390520/ENST00000390520.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000390520/ENST00000390520.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000390520/deletion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000400151/ENST00000400151.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000400151/ENST00000400151.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000400151/long-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000409523/ENST00000409523.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000409523/ENST00000409523.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000409523/long-overlapping-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009/ENST00000410009.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009/ENST00000410009.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009/frameshift.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000413103/ENST00000413103.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000413103/ENST00000413103.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000413103/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420190/ENST00000420190.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420190/ENST00000420190.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420190/abort-in-csq-push.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/segfault.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/start-stop-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000422159 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000436063/ENST00000436063.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000436063/ENST00000436063.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000436063/insert-before-utr.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000448695/ENST00000448695.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000448695/ENST00000448695.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414/ENST00000518414.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414/ENST00000518414.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000519442/ENST00000519442.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000519442/ENST00000519442.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000519442/synon-splice-region-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520868/ENST00000520868.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520868/ENST00000520868.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520868/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000528237/ENST00000528237.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000528237/ENST00000528237.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000545279/ENST00000545279.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000545279/ENST00000545279.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000545279/splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000557788/ENST00000557788.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000557788/ENST00000557788.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000557788/long-overlap-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000580206 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000593942/ENST00000593942.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000593942/ENST00000593942.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000593942/last-codon-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000624631/ENST00000624631.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000624631/ENST00000624631.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000624631/ambiguous.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/UDLPM26cBc/gtcheck.1.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,GT /tmp/UDLPM26cBc/gtcheck.1.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,PL /tmp/UDLPM26cBc/gtcheck.1.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,GT /tmp/UDLPM26cBc/gtcheck.1.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,PL /tmp/UDLPM26cBc/gtcheck.1.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -p s1,s1 /tmp/UDLPM26cBc/gtcheck.1.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/UDLPM26cBc/gtcheck.2.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/UDLPM26cBc/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/UDLPM26cBc/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gtcheck.3.pairs /tmp/UDLPM26cBc/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL /tmp/UDLPM26cBc/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 --n-matches 4 /tmp/UDLPM26cBc/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/UDLPM26cBc/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/UDLPM26cBc/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/UDLPM26cBc/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/UDLPM26cBc/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/UDLPM26cBc/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -p B,C,B,D /tmp/UDLPM26cBc/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,GT -H /tmp/UDLPM26cBc/gtcheck.1.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,PL -H /tmp/UDLPM26cBc/gtcheck.1.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,GT -H /tmp/UDLPM26cBc/gtcheck.1.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,PL -H /tmp/UDLPM26cBc/gtcheck.1.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/UDLPM26cBc/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/UDLPM26cBc/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -u GT -e 30 /tmp/UDLPM26cBc/gtcheck.1.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/UDLPM26cBc/gtcheck.1.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -u GT -e 300 /tmp/UDLPM26cBc/gtcheck.1.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -u PL -e 30 /tmp/UDLPM26cBc/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck /tmp/UDLPM26cBc/gtcheck.ntop.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck --n-matches 2 /tmp/UDLPM26cBc/gtcheck.ntop.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck /tmp/UDLPM26cBc/gtcheck.5.vcf.gz -g /tmp/UDLPM26cBc/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok Number of tests: total .. 1723 passed .. 1723 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: bcftools-1.15.1-11.fc41.i686 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.QEH9P1 + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + cd bcftools-1.15.1 + DOCDIR=/builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/doc/bcftools + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/doc/bcftools + cp -pr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/AUTHORS /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/doc/bcftools + cp -pr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/NEWS /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/doc/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.pvYmlq + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + cd bcftools-1.15.1 + LICENSEDIR=/builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/licenses/bcftools + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/licenses/bcftools + cp -pr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/LICENSE /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/licenses/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Provides: bcftools = 1.15.1-11.fc41 bcftools(x86-32) = 1.15.1-11.fc41 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_2.38) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libc.so.6(GLIBC_ABI_DT_RELR) libgsl.so.27 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.5.40 libz.so.1 rtld(GNU_HASH) Conflicts: samtools < 1.0 Processing files: bcftools-debugsource-1.15.1-11.fc41.i686 Provides: bcftools-debugsource = 1.15.1-11.fc41 bcftools-debugsource(x86-32) = 1.15.1-11.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bcftools-debuginfo-1.15.1-11.fc41.i686 Provides: bcftools-debuginfo = 1.15.1-11.fc41 bcftools-debuginfo(x86-32) = 1.15.1-11.fc41 debuginfo(build-id) = 014c95bbdf4e7432d0cff08073836ea8203223e7 debuginfo(build-id) = 031875081672da35775332ff501a564028d9ff1c debuginfo(build-id) = 04f47fb2fd84d334d5b4a655d918ee116f3a6af9 debuginfo(build-id) = 06978bdaa09b86fe1bd58d4cfa29aa948e9adf4e debuginfo(build-id) = 0707f346cc74951dd357cf16716cd3d2c8c5e324 debuginfo(build-id) = 0a2aae021c0f6843778b0733a4dbfc83628a71ff debuginfo(build-id) = 0a7cf66cf837fca3f955f7c036f6d7781ec36f6d debuginfo(build-id) = 0fc9fcdd466fd4c6efd02147c4e5684888ca7fe2 debuginfo(build-id) = 0fe286d722e0514a165861293a946bb6814c3078 debuginfo(build-id) = 1a1c2cccd04be83adf994751e0a84bcce35e2c7f debuginfo(build-id) = 1b2d8893cb4ef054430b91bb10c69f8d8794af36 debuginfo(build-id) = 282a893e2bc672735af967b86d05ee0eedde09ac debuginfo(build-id) = 54e8be578a6dd5a77b39861a1b91ebc92dcba49d debuginfo(build-id) = 5eb0af154679dd83940e876db3c97fe9e9eb3765 debuginfo(build-id) = 5ee8dc42acea7d99134a48729492387a72368197 debuginfo(build-id) = 6d257ab147e7c19c28907601876eedfc76cb50a6 debuginfo(build-id) = 7859641ac6979c4ed5503a8b37ec1a71d057b428 debuginfo(build-id) = 863fea986daac1abc7822e9f3fd7fc2f3785efbc debuginfo(build-id) = 8b662d865c6d2fcd6090697b05df1cb1d5cb7ad9 debuginfo(build-id) = 8dc5a28a6534808dc56d8bcd297c8aed62992cc1 debuginfo(build-id) = 902e3004bd1ff8e44ca30669394975d66d7c2fc6 debuginfo(build-id) = 94c429ff797315068eff82b399b63a2e44568ded debuginfo(build-id) = 9a7ef4f8e8091e9661256184915baa5df505d120 debuginfo(build-id) = a9967a3dda6442e65864cbb2a8c7659dec0f3737 debuginfo(build-id) = adf18c8e69a65f2e3d7f89fed2e059d6942e4e54 debuginfo(build-id) = b765dd9e963887fc134585c3dba9cf048cd42bb2 debuginfo(build-id) = b991b5055f7f95908f2638822b0ca67a54efe01f debuginfo(build-id) = bc2b267c5bdf6d70368d707db60f0e0130272f56 debuginfo(build-id) = bce1206effe8e26fbe2f8f98794f376bc689a1a3 debuginfo(build-id) = c47b0dc56ac4208a8312d114790d95680d46d37d debuginfo(build-id) = c54eaedc0b8c3f2ebd26287af42e3c3a6c39d9b5 debuginfo(build-id) = c6615a98ea316a4a5b445e79fa0c6d4ae41890e3 debuginfo(build-id) = e3435c32474c002b78abbaa215800bda73b31210 debuginfo(build-id) = ec086031b4e49b67c5acb13123f6d40e56ba65ea debuginfo(build-id) = ee963fc3479a7bc42f7903001d09cae94fc4d476 debuginfo(build-id) = ee9bde390184a577f47ad22421e6b43f115e6d4f debuginfo(build-id) = fd719e5c5722a92c0d963c88a49a62ba784a9fb7 debuginfo(build-id) = fe12ce169371985a1b89ef1e57bf493c25bc4fe4 debuginfo(build-id) = ff2018ab7a2e6825063b9dcc94dbed53b75ef70c Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bcftools-debugsource(x86-32) = 1.15.1-11.fc41 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT Wrote: /builddir/build/RPMS/bcftools-1.15.1-11.fc41.i686.rpm Wrote: /builddir/build/RPMS/bcftools-debugsource-1.15.1-11.fc41.i686.rpm Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.15.1-11.fc41.i686.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.VqwyHL + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + test -d /builddir/build/BUILD/bcftools-1.15.1-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/bcftools-1.15.1-build + rm -rf /builddir/build/BUILD/bcftools-1.15.1-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild bcftools-1.15.1-11.fc41.src.rpm Finish: build phase for bcftools-1.15.1-11.fc41.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-41-i686-1737371804.483416/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names INFO: Done(/var/lib/copr-rpmbuild/results/bcftools-1.15.1-11.fc41.src.rpm) Config(child) 1 minutes 12 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "bcftools", "epoch": null, "version": "1.15.1", "release": "11.fc41", "arch": "i686" }, { "name": "bcftools", "epoch": null, "version": "1.15.1", "release": "11.fc41", "arch": "src" }, { "name": "bcftools-debugsource", "epoch": null, "version": "1.15.1", "release": "11.fc41", "arch": "i686" }, { "name": "bcftools-debuginfo", "epoch": null, "version": "1.15.1", "release": "11.fc41", "arch": "i686" } ] } RPMResults finished