Warning: Permanently added '34.228.240.188' (ED25519) to the list of known hosts. Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-apvukow1/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-apvukow1/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1733546906.841703 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.9 starting (python version = 3.13.0, NVR = mock-5.9-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-apvukow1/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-apvukow1/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1733546906.841703 -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-apvukow1/bcftools/bcftools.spec) Config(fedora-rawhide-aarch64) Start: clean chroot Finish: clean chroot Mock Version: 5.9 INFO: Mock Version: 5.9 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1733546906.841703/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1733546906.841703/root INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/cb01a00c029bda66d23831623a5e4fead1241a29f29b03c91285d60b89df4ef7/merged INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/cb01a00c029bda66d23831623a5e4fead1241a29f29b03c91285d60b89df4ef7/merged) with podman image umount INFO: Package manager dnf5 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-1733546906.841703/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.fc42.aarch64 rpm-sequoia-1.7.0-2.fc41.aarch64 dnf5-5.2.7.0-1.fc42.aarch64 dnf5-plugins-5.2.7.0-1.fc42.aarch64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 258.3 KiB/s | 13.4 KiB | 00m00s Copr repository 100% | 102.1 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 22.5 MiB/s | 784.9 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash aarch64 5.2.37-1.fc42 fedora 8.2 MiB bzip2 aarch64 1.0.8-19.fc41 fedora 427.6 KiB coreutils aarch64 9.5-11.fc42 fedora 8.1 MiB cpio aarch64 2.15-2.fc41 fedora 1.2 MiB diffutils aarch64 3.10-8.fc41 fedora 2.1 MiB fedora-release-common noarch 42-0.11 fedora 19.8 KiB findutils aarch64 1:4.10.0-4.fc41 fedora 2.1 MiB gawk aarch64 5.3.0-4.fc41 fedora 4.2 MiB glibc-minimal-langpack aarch64 2.40.9000-21.fc42 fedora 0.0 B grep aarch64 3.11-9.fc41 fedora 1.1 MiB gzip aarch64 1.13-2.fc41 fedora 488.9 KiB info aarch64 7.1.1-2.fc42 fedora 613.6 KiB patch aarch64 2.7.6-25.fc41 fedora 390.6 KiB redhat-rpm-config noarch 296-1.fc42 fedora 186.6 KiB rpm-build aarch64 4.20.0-1.fc42 fedora 1.4 MiB sed aarch64 4.9-3.fc41 fedora 1.0 MiB shadow-utils aarch64 2:4.16.0-7.fc42 fedora 5.0 MiB tar aarch64 2:1.35-4.fc41 fedora 3.1 MiB unzip aarch64 6.0-65.fc42 fedora 2.3 MiB util-linux aarch64 2.40.2-8.fc42 fedora 16.9 MiB which aarch64 2.21-42.fc41 fedora 248.2 KiB xz aarch64 1:5.6.3-2.fc42 fedora 1.5 MiB Installing dependencies: add-determinism aarch64 0.4.3-1.fc42 fedora 2.1 MiB alternatives aarch64 1.30-1.fc41 fedora 218.3 KiB ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB audit-libs aarch64 4.0.2-1.fc42 copr_base 415.2 KiB authselect aarch64 1.5.0-8.fc42 copr_base 179.9 KiB authselect-libs aarch64 1.5.0-8.fc42 copr_base 865.5 KiB basesystem noarch 11-21.fc41 fedora 0.0 B binutils aarch64 2.43.50-9.fc42 fedora 29.4 MiB build-reproducibility-srpm-macros noarch 0.4.3-1.fc42 fedora 735.0 B bzip2-libs aarch64 1.0.8-19.fc41 fedora 200.7 KiB ca-certificates noarch 2024.2.69_v8.0.401-3.fc42 fedora 2.6 MiB coreutils-common aarch64 9.5-11.fc42 fedora 11.2 MiB cracklib aarch64 2.9.11-6.fc41 fedora 935.0 KiB crypto-policies noarch 20241128-1.gitbb7b0b0.fc42 fedora 137.3 KiB curl aarch64 8.10.1-2.fc42 fedora 581.3 KiB cyrus-sasl-lib aarch64 2.1.28-27.fc41 fedora 3.1 MiB debugedit aarch64 5.1-2.fc42 fedora 244.2 KiB dwz aarch64 0.15-8.fc42 fedora 386.8 KiB ed aarch64 1.20.2-2.fc41 fedora 282.8 KiB efi-srpm-macros noarch 5-13.fc42 fedora 40.2 KiB elfutils aarch64 0.192-7.fc42 fedora 3.1 MiB elfutils-debuginfod-client aarch64 0.192-7.fc42 fedora 141.3 KiB elfutils-default-yama-scope noarch 0.192-7.fc42 fedora 1.8 KiB elfutils-libelf aarch64 0.192-7.fc42 fedora 1.2 MiB elfutils-libs aarch64 0.192-7.fc42 fedora 734.9 KiB fedora-gpg-keys noarch 42-0.3 fedora 126.4 KiB fedora-release noarch 42-0.11 fedora 0.0 B fedora-release-identity-basic noarch 42-0.11 fedora 719.0 B fedora-repos noarch 42-0.3 fedora 4.9 KiB fedora-repos-rawhide noarch 42-0.3 fedora 2.2 KiB file aarch64 5.45-8.fc42 fedora 139.5 KiB file-libs aarch64 5.45-8.fc42 fedora 10.0 MiB filesystem aarch64 3.18-29.fc42 fedora 106.0 B fonts-srpm-macros noarch 1:2.0.5-17.fc41 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-1.fc42 fedora 38.9 KiB fpc-srpm-macros noarch 1.3-13.fc41 fedora 144.0 B gdb-minimal aarch64 15.2-3.fc42 fedora 13.2 MiB gdbm aarch64 1:1.23-7.fc41 fedora 928.5 KiB gdbm-libs aarch64 1:1.23-7.fc41 fedora 426.0 KiB ghc-srpm-macros noarch 1.9.2-1.fc42 fedora 779.0 B glibc aarch64 2.40.9000-21.fc42 fedora 6.1 MiB glibc-common aarch64 2.40.9000-21.fc42 fedora 1.3 MiB glibc-gconv-extra aarch64 2.40.9000-21.fc42 fedora 18.3 MiB gmp aarch64 1:6.3.0-2.fc41 fedora 722.0 KiB gnat-srpm-macros noarch 6-6.fc41 fedora 1.0 KiB go-srpm-macros noarch 3.6.0-5.fc42 fedora 60.8 KiB jansson aarch64 2.14-1.fc42 fedora 221.3 KiB json-c aarch64 0.18-1.fc42 fedora 139.2 KiB kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB keyutils-libs aarch64 1.6.3-4.fc41 fedora 226.4 KiB krb5-libs aarch64 1.21.3-3.fc42 fedora 2.6 MiB libacl aarch64 2.3.2-2.fc42 copr_base 66.3 KiB libarchive aarch64 3.7.7-1.fc42 fedora 912.2 KiB libattr aarch64 2.5.2-4.fc41 fedora 196.6 KiB libblkid aarch64 2.40.2-8.fc42 fedora 418.6 KiB libbrotli aarch64 1.1.0-5.fc41 fedora 1.1 MiB libcap aarch64 2.71-1.fc42 fedora 509.8 KiB libcap-ng aarch64 0.8.5-3.fc41 fedora 417.2 KiB libcom_err aarch64 1.47.1-6.fc42 fedora 239.3 KiB libcurl aarch64 8.10.1-2.fc42 fedora 858.4 KiB libeconf aarch64 0.7.4-3.fc42 fedora 85.7 KiB libevent aarch64 2.1.12-14.fc41 fedora 1.5 MiB libfdisk aarch64 2.40.2-8.fc42 fedora 482.9 KiB libffi aarch64 3.4.6-3.fc42 fedora 282.4 KiB libgcc aarch64 14.2.1-6.fc42 fedora 222.2 KiB libgomp aarch64 14.2.1-6.fc42 fedora 503.2 KiB libidn2 aarch64 2.3.7-2.fc41 fedora 457.2 KiB libmount aarch64 2.40.2-8.fc42 fedora 483.9 KiB libnghttp2 aarch64 1.64.0-1.fc42 fedora 262.2 KiB libnsl2 aarch64 2.0.1-2.fc41 fedora 222.0 KiB libpkgconf aarch64 2.3.0-1.fc42 fedora 198.1 KiB libpsl aarch64 0.21.5-4.fc41 fedora 196.6 KiB libpwquality aarch64 1.4.5-11.fc41 fedora 1.1 MiB libselinux aarch64 3.8-0.rc1.2.fc42 fedora 195.6 KiB libsemanage aarch64 3.8-0.rc1.1.fc42 fedora 353.3 KiB libsepol aarch64 3.8-0.rc1.1.fc42 fedora 809.9 KiB libsmartcols aarch64 2.40.2-8.fc42 fedora 288.5 KiB libssh aarch64 0.11.1-1.fc42 fedora 649.6 KiB libssh-config noarch 0.11.1-1.fc42 fedora 277.0 B libstdc++ aarch64 14.2.1-6.fc42 fedora 2.8 MiB libtasn1 aarch64 4.19.0-9.fc41 fedora 283.8 KiB libtirpc aarch64 1.3.6-1.fc42 fedora 212.9 KiB libtool-ltdl aarch64 2.4.7-12.fc41 fedora 222.2 KiB libunistring aarch64 1.1-8.fc41 fedora 1.8 MiB libuuid aarch64 2.40.2-8.fc42 fedora 197.5 KiB libverto aarch64 0.3.2-9.fc41 fedora 197.5 KiB libxcrypt aarch64 4.4.36-11.fc42 fedora 271.5 KiB libxml2 aarch64 2.12.8-2.fc41 fedora 2.1 MiB libzstd aarch64 1.5.6-2.fc41 fedora 796.0 KiB lua-libs aarch64 5.4.7-1.fc42 fedora 393.1 KiB lua-srpm-macros noarch 1-14.fc41 fedora 1.3 KiB lz4-libs aarch64 1.10.0-1.fc41 fedora 261.6 KiB mpfr aarch64 4.2.1-5.fc41 fedora 818.9 KiB ncurses-base noarch 6.5-2.20240629.fc41 fedora 326.3 KiB ncurses-libs aarch64 6.5-2.20240629.fc41 fedora 2.2 MiB ocaml-srpm-macros noarch 10-3.fc41 fedora 1.9 KiB openblas-srpm-macros noarch 2-18.fc41 fedora 112.0 B openldap aarch64 2.6.8-6.fc42 fedora 747.0 KiB openssl-libs aarch64 1:3.2.2-8.fc42 fedora 7.2 MiB p11-kit aarch64 0.25.5-4.fc42 fedora 2.6 MiB p11-kit-trust aarch64 0.25.5-4.fc42 fedora 655.7 KiB package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB pam aarch64 1.7.0-3.fc42 fedora 4.3 MiB pam-libs aarch64 1.7.0-3.fc42 fedora 223.4 KiB pcre2 aarch64 10.44-1.fc41.1 fedora 905.5 KiB pcre2-syntax noarch 10.44-1.fc41.1 fedora 251.6 KiB perl-srpm-macros noarch 1-56.fc41 fedora 861.0 B pkgconf aarch64 2.3.0-1.fc42 fedora 240.6 KiB pkgconf-m4 noarch 2.3.0-1.fc42 fedora 14.4 KiB pkgconf-pkg-config aarch64 2.3.0-1.fc42 fedora 990.0 B popt aarch64 1.19-7.fc41 fedora 272.9 KiB publicsuffix-list-dafsa noarch 20240107-4.fc41 fedora 67.5 KiB pyproject-srpm-macros noarch 1.16.3-1.fc42 fedora 1.9 KiB python-srpm-macros noarch 3.13-3.fc41 fedora 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc42 fedora 500.0 B qt6-srpm-macros noarch 6.8.0-1.fc42 fedora 456.0 B readline aarch64 8.2-11.fc42 fedora 753.3 KiB rpm aarch64 4.20.0-1.fc42 fedora 3.9 MiB rpm-build-libs aarch64 4.20.0-1.fc42 fedora 262.7 KiB rpm-libs aarch64 4.20.0-1.fc42 fedora 797.9 KiB rpm-sequoia aarch64 1.7.0-2.fc41 fedora 2.3 MiB rust-srpm-macros noarch 26.3-3.fc42 fedora 4.8 KiB setup noarch 2.15.0-5.fc41 fedora 720.7 KiB sqlite-libs aarch64 3.47.1-1.fc42 fedora 1.4 MiB systemd-libs aarch64 257~rc3-1.fc42 fedora 2.5 MiB util-linux-core aarch64 2.40.2-8.fc42 fedora 6.2 MiB xxhash-libs aarch64 0.8.2-4.fc42 fedora 212.3 KiB xz-libs aarch64 1:5.6.3-2.fc42 fedora 266.4 KiB zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB zip aarch64 3.0-41.fc41 fedora 1.1 MiB zlib-ng-compat aarch64 2.2.2-1.fc42 fedora 133.8 KiB zstd aarch64 1.5.6-2.fc41 fedora 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 154 packages Total size of inbound packages is 52 MiB. Need to download 0 B. After this operation, 238 MiB extra will be used (install 238 MiB, remove 0 B). [1/1] tar-2:1.35-4.fc41.aarch64 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] bzip2-0:1.0.8-19.fc41.aarch64 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] redhat-rpm-config-0:296-1.fc42.no 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] rpm-build-0:4.20.0-1.fc42.aarch64 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] unzip-0:6.0-65.fc42.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded 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100% | 0.0 B/s | 0.0 B | 00m00s [ 1/149] libunistring-0:1.1-8.fc41.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already 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-0:0.11.1-1.fc42 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.aar 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 Importing PGP key 0x105EF944: UserID : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing PGP key 0x105EF944: UserID : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing PGP key 0xE99D6AD1: UserID : "Fedora (41) " Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary The key was successfully imported. Importing PGP key 0x31645531: UserID : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. [ 1/156] Verify package files 100% | 719.0 B/s | 154.0 B | 00m00s >>> Running pre-transaction scriptlet: filesystem-0:3.18-29.fc42.aarch64 >>> Finished pre-transaction scriptlet: filesystem-0:3.18-29.fc42.aarch64 >>> [RPM] /var/lib/mock/fedora-rawhide-aarch64-1733546906.841703/root/var/cache/ [ 2/156] Prepare transaction 100% | 2.5 KiB/s | 154.0 B | 00m00s [ 3/156] Installing libgcc-0:14.2.1-6. 100% | 109.3 MiB/s | 223.9 KiB | 00m00s [ 4/156] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 5/156] Installing publicsuffix-list- 100% | 66.7 MiB/s | 68.3 KiB | 00m00s [ 6/156] Installing fedora-release-ide 100% | 953.1 KiB/s | 976.0 B | 00m00s [ 7/156] Installing fedora-gpg-keys-0: 100% | 28.0 MiB/s | 172.2 KiB | 00m00s [ 8/156] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.4 KiB | 00m00s [ 9/156] Installing fedora-repos-0:42- 100% | 0.0 B/s | 5.7 KiB | 00m00s [ 10/156] Installing fedora-release-com 100% | 23.6 MiB/s | 24.1 KiB | 00m00s [ 11/156] Installing 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193.2 KiB | 00m00s [151/156] Installing rpm-build-0:4.20.0 100% | 349.3 MiB/s | 1.4 MiB | 00m00s [152/156] Installing pyproject-srpm-mac 100% | 1.2 MiB/s | 2.5 KiB | 00m00s [153/156] Installing util-linux-0:2.40. 100% | 368.6 MiB/s | 17.0 MiB | 00m00s [154/156] Installing authselect-0:1.5.0 100% | 60.0 MiB/s | 184.3 KiB | 00m00s [155/156] Installing which-0:2.21-42.fc 100% | 122.2 MiB/s | 250.4 KiB | 00m00s [156/156] Installing info-0:7.1.1-2.fc4 100% | 284.4 KiB/s | 614.0 KiB | 00m02s Warning: skipped PGP checks for 4 packages from repository: copr_base Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.4.3-1.fc42.aarch64 alternatives-1.30-1.fc41.aarch64 ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.2-1.fc42.aarch64 authselect-1.5.0-8.fc42.aarch64 authselect-libs-1.5.0-8.fc42.aarch64 basesystem-11-21.fc41.noarch bash-5.2.37-1.fc42.aarch64 binutils-2.43.50-9.fc42.aarch64 build-reproducibility-srpm-macros-0.4.3-1.fc42.noarch bzip2-1.0.8-19.fc41.aarch64 bzip2-libs-1.0.8-19.fc41.aarch64 ca-certificates-2024.2.69_v8.0.401-3.fc42.noarch coreutils-9.5-11.fc42.aarch64 coreutils-common-9.5-11.fc42.aarch64 cpio-2.15-2.fc41.aarch64 cracklib-2.9.11-6.fc41.aarch64 crypto-policies-20241128-1.gitbb7b0b0.fc42.noarch curl-8.10.1-2.fc42.aarch64 cyrus-sasl-lib-2.1.28-27.fc41.aarch64 debugedit-5.1-2.fc42.aarch64 diffutils-3.10-8.fc41.aarch64 dwz-0.15-8.fc42.aarch64 ed-1.20.2-2.fc41.aarch64 efi-srpm-macros-5-13.fc42.noarch elfutils-0.192-7.fc42.aarch64 elfutils-debuginfod-client-0.192-7.fc42.aarch64 elfutils-default-yama-scope-0.192-7.fc42.noarch elfutils-libelf-0.192-7.fc42.aarch64 elfutils-libs-0.192-7.fc42.aarch64 fedora-gpg-keys-42-0.3.noarch fedora-release-42-0.11.noarch fedora-release-common-42-0.11.noarch fedora-release-identity-basic-42-0.11.noarch fedora-repos-42-0.3.noarch fedora-repos-rawhide-42-0.3.noarch file-5.45-8.fc42.aarch64 file-libs-5.45-8.fc42.aarch64 filesystem-3.18-29.fc42.aarch64 findutils-4.10.0-4.fc41.aarch64 fonts-srpm-macros-2.0.5-17.fc41.noarch forge-srpm-macros-0.4.0-1.fc42.noarch fpc-srpm-macros-1.3-13.fc41.noarch gawk-5.3.0-4.fc41.aarch64 gdb-minimal-15.2-3.fc42.aarch64 gdbm-1.23-7.fc41.aarch64 gdbm-libs-1.23-7.fc41.aarch64 ghc-srpm-macros-1.9.2-1.fc42.noarch glibc-2.40.9000-21.fc42.aarch64 glibc-common-2.40.9000-21.fc42.aarch64 glibc-gconv-extra-2.40.9000-21.fc42.aarch64 glibc-minimal-langpack-2.40.9000-21.fc42.aarch64 gmp-6.3.0-2.fc41.aarch64 gnat-srpm-macros-6-6.fc41.noarch go-srpm-macros-3.6.0-5.fc42.noarch gpg-pubkey-105ef944-65ca83d1 gpg-pubkey-31645531-66b6dccf gpg-pubkey-e99d6ad1-64d2612c grep-3.11-9.fc41.aarch64 gzip-1.13-2.fc41.aarch64 info-7.1.1-2.fc42.aarch64 jansson-2.14-1.fc42.aarch64 json-c-0.18-1.fc42.aarch64 kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc41.aarch64 krb5-libs-1.21.3-3.fc42.aarch64 libacl-2.3.2-2.fc42.aarch64 libarchive-3.7.7-1.fc42.aarch64 libattr-2.5.2-4.fc41.aarch64 libblkid-2.40.2-8.fc42.aarch64 libbrotli-1.1.0-5.fc41.aarch64 libcap-2.71-1.fc42.aarch64 libcap-ng-0.8.5-3.fc41.aarch64 libcom_err-1.47.1-6.fc42.aarch64 libcurl-8.10.1-2.fc42.aarch64 libeconf-0.7.4-3.fc42.aarch64 libevent-2.1.12-14.fc41.aarch64 libfdisk-2.40.2-8.fc42.aarch64 libffi-3.4.6-3.fc42.aarch64 libgcc-14.2.1-6.fc42.aarch64 libgomp-14.2.1-6.fc42.aarch64 libidn2-2.3.7-2.fc41.aarch64 libmount-2.40.2-8.fc42.aarch64 libnghttp2-1.64.0-1.fc42.aarch64 libnsl2-2.0.1-2.fc41.aarch64 libpkgconf-2.3.0-1.fc42.aarch64 libpsl-0.21.5-4.fc41.aarch64 libpwquality-1.4.5-11.fc41.aarch64 libselinux-3.8-0.rc1.2.fc42.aarch64 libsemanage-3.8-0.rc1.1.fc42.aarch64 libsepol-3.8-0.rc1.1.fc42.aarch64 libsmartcols-2.40.2-8.fc42.aarch64 libssh-0.11.1-1.fc42.aarch64 libssh-config-0.11.1-1.fc42.noarch libstdc++-14.2.1-6.fc42.aarch64 libtasn1-4.19.0-9.fc41.aarch64 libtirpc-1.3.6-1.fc42.aarch64 libtool-ltdl-2.4.7-12.fc41.aarch64 libunistring-1.1-8.fc41.aarch64 libuuid-2.40.2-8.fc42.aarch64 libverto-0.3.2-9.fc41.aarch64 libxcrypt-4.4.36-11.fc42.aarch64 libxml2-2.12.8-2.fc41.aarch64 libzstd-1.5.6-2.fc41.aarch64 lua-libs-5.4.7-1.fc42.aarch64 lua-srpm-macros-1-14.fc41.noarch lz4-libs-1.10.0-1.fc41.aarch64 mpfr-4.2.1-5.fc41.aarch64 ncurses-base-6.5-2.20240629.fc41.noarch ncurses-libs-6.5-2.20240629.fc41.aarch64 ocaml-srpm-macros-10-3.fc41.noarch openblas-srpm-macros-2-18.fc41.noarch openldap-2.6.8-6.fc42.aarch64 openssl-libs-3.2.2-8.fc42.aarch64 p11-kit-0.25.5-4.fc42.aarch64 p11-kit-trust-0.25.5-4.fc42.aarch64 package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.7.0-3.fc42.aarch64 pam-libs-1.7.0-3.fc42.aarch64 patch-2.7.6-25.fc41.aarch64 pcre2-10.44-1.fc41.1.aarch64 pcre2-syntax-10.44-1.fc41.1.noarch perl-srpm-macros-1-56.fc41.noarch pkgconf-2.3.0-1.fc42.aarch64 pkgconf-m4-2.3.0-1.fc42.noarch pkgconf-pkg-config-2.3.0-1.fc42.aarch64 popt-1.19-7.fc41.aarch64 publicsuffix-list-dafsa-20240107-4.fc41.noarch pyproject-srpm-macros-1.16.3-1.fc42.noarch python-srpm-macros-3.13-3.fc41.noarch qt5-srpm-macros-5.15.15-1.fc42.noarch qt6-srpm-macros-6.8.0-1.fc42.noarch readline-8.2-11.fc42.aarch64 redhat-rpm-config-296-1.fc42.noarch rpm-4.20.0-1.fc42.aarch64 rpm-build-4.20.0-1.fc42.aarch64 rpm-build-libs-4.20.0-1.fc42.aarch64 rpm-libs-4.20.0-1.fc42.aarch64 rpm-sequoia-1.7.0-2.fc41.aarch64 rust-srpm-macros-26.3-3.fc42.noarch sed-4.9-3.fc41.aarch64 setup-2.15.0-5.fc41.noarch shadow-utils-4.16.0-7.fc42.aarch64 sqlite-libs-3.47.1-1.fc42.aarch64 systemd-libs-257~rc3-1.fc42.aarch64 tar-1.35-4.fc41.aarch64 unzip-6.0-65.fc42.aarch64 util-linux-2.40.2-8.fc42.aarch64 util-linux-core-2.40.2-8.fc42.aarch64 which-2.21-42.fc41.aarch64 xxhash-libs-0.8.2-4.fc42.aarch64 xz-5.6.3-2.fc42.aarch64 xz-libs-5.6.3-2.fc42.aarch64 zig-srpm-macros-1-3.fc41.noarch zip-3.0-41.fc41.aarch64 zlib-ng-compat-2.2.2-1.fc42.aarch64 zstd-1.5.6-2.fc41.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721174400 Wrote: /builddir/build/SRPMS/bcftools-1.15.1-10.fc42.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-aarch64-1733546906.841703/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-apvukow1/bcftools/bcftools.spec) Config(child) 0 minutes 11 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/bcftools-1.15.1-10.fc42.src.rpm) Config(fedora-rawhide-aarch64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1733546906.841703/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1733546906.841703/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-1733546906.841703/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.fc42.aarch64 rpm-sequoia-1.7.0-2.fc41.aarch64 dnf5-5.2.7.0-1.fc42.aarch64 dnf5-plugins-5.2.7.0-1.fc42.aarch64 Finish: chroot init Start: build phase for bcftools-1.15.1-10.fc42.src.rpm Start: build setup for bcftools-1.15.1-10.fc42.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721174400 Wrote: /builddir/build/SRPMS/bcftools-1.15.1-10.fc42.src.rpm Updating and loading repositories: fedora 100% | 274.1 KiB/s | 13.4 KiB | 00m00s Copr repository 100% | 109.4 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: gcc aarch64 14.2.1-6.fc42 fedora 96.6 MiB gsl-devel aarch64 2.7.1-11.fc41 fedora 1.6 MiB htslib-devel aarch64 1.15.1-6.fc41 fedora 411.0 KiB htslib-tools aarch64 1.15.1-6.fc41 fedora 2.5 MiB make aarch64 1:4.4.1-9.fc42 fedora 1.8 MiB perl-ExtUtils-Embed noarch 1.35-512.fc42 fedora 15.5 KiB perl-File-Temp noarch 1:0.231.100-511.fc41 fedora 162.3 KiB perl-FindBin noarch 1.54-512.fc42 fedora 6.7 KiB perl-Getopt-Long noarch 1:2.58-2.fc41 fedora 144.5 KiB perl-interpreter aarch64 4:5.40.0-512.fc42 fedora 302.3 KiB zlib-ng-compat-devel aarch64 2.2.2-1.fc42 fedora 106.8 KiB Installing dependencies: annobin-docs noarch 12.77-1.fc42 copr_base 98.4 KiB annobin-plugin-gcc aarch64 12.77-1.fc42 copr_base 997.1 KiB autoconf noarch 2.72-3.fc42 copr_base 2.8 MiB automake noarch 1.17-1.fc42 copr_base 1.8 MiB cmake-filesystem aarch64 3.31.1-1.fc42 fedora 0.0 B cpp aarch64 14.2.1-6.fc42 fedora 33.7 MiB emacs-filesystem noarch 1:30.0-3.fc41 fedora 0.0 B expat aarch64 2.6.4-1.fc42 fedora 349.3 KiB gcc-plugin-annobin aarch64 14.2.1-6.fc42 fedora 73.5 KiB glibc-devel aarch64 2.40.9000-21.fc42 fedora 2.2 MiB groff-base aarch64 1.23.0-7.fc41 fedora 5.2 MiB gsl aarch64 2.7.1-11.fc41 fedora 3.7 MiB htslib aarch64 1.15.1-6.fc41 fedora 1.8 MiB kernel-headers aarch64 6.13.0-0.rc1.e70140ba0d2b.14.fc42 fedora 6.4 MiB libasan aarch64 14.2.1-6.fc42 fedora 1.5 MiB libatomic aarch64 14.2.1-6.fc42 fedora 69.0 KiB libb2 aarch64 0.98.1-12.fc41 fedora 202.2 KiB libmpc aarch64 1.3.1-6.fc41 fedora 280.8 KiB libubsan aarch64 14.2.1-6.fc42 fedora 475.2 KiB libxcrypt-devel aarch64 4.4.36-11.fc42 fedora 30.5 KiB m4 aarch64 1.4.19-10.fc41 fedora 668.7 KiB mpdecimal aarch64 2.5.1-16.fc41 fedora 328.9 KiB ncurses aarch64 6.5-2.20240629.fc41 fedora 1.7 MiB perl-AutoLoader noarch 5.74-512.fc42 fedora 20.5 KiB perl-AutoSplit noarch 5.74-512.fc42 fedora 23.1 KiB perl-B aarch64 1.89-512.fc42 fedora 606.1 KiB perl-Benchmark noarch 1.25-512.fc42 fedora 36.3 KiB perl-Carp noarch 1.54-511.fc41 fedora 46.6 KiB perl-Class-Struct noarch 0.68-512.fc42 fedora 25.4 KiB perl-Data-Dumper aarch64 2.189-512.fc41 fedora 263.8 KiB perl-Devel-PPPort aarch64 3.72-512.fc41 fedora 980.3 KiB perl-Digest noarch 1.20-511.fc41 fedora 35.3 KiB perl-Digest-MD5 aarch64 2.59-5.fc41 fedora 231.9 KiB perl-DynaLoader aarch64 1.56-512.fc42 fedora 32.1 KiB perl-Encode aarch64 4:3.21-511.fc41 fedora 5.9 MiB perl-Errno aarch64 1.38-512.fc42 fedora 8.4 KiB perl-Exporter noarch 5.78-511.fc41 fedora 54.3 KiB perl-ExtUtils-Command noarch 2:7.70-512.fc41 fedora 9.6 KiB perl-ExtUtils-Constant noarch 0.25-512.fc42 fedora 85.8 KiB perl-ExtUtils-Install noarch 2.22-511.fc41 fedora 85.5 KiB perl-ExtUtils-MakeMaker noarch 2:7.70-512.fc41 fedora 734.1 KiB perl-ExtUtils-Manifest noarch 1:1.75-511.fc41 fedora 84.8 KiB perl-ExtUtils-ParseXS noarch 1:3.51-511.fc41 fedora 399.7 KiB perl-Fcntl aarch64 1.18-512.fc42 fedora 221.1 KiB perl-File-Basename noarch 2.86-512.fc42 fedora 14.0 KiB perl-File-Compare noarch 1.100.800-512.fc42 fedora 5.6 KiB perl-File-Copy noarch 2.41-512.fc42 fedora 19.6 KiB perl-File-Find noarch 1.44-512.fc42 fedora 41.9 KiB perl-File-Path noarch 2.18-511.fc41 fedora 63.5 KiB perl-File-stat noarch 1.14-512.fc42 fedora 12.5 KiB perl-FileHandle noarch 2.05-512.fc42 fedora 9.3 KiB perl-Getopt-Std noarch 1.14-512.fc42 fedora 11.2 KiB perl-HTTP-Tiny noarch 0.090-1.fc42 fedora 154.4 KiB perl-IO aarch64 1.55-512.fc42 fedora 319.2 KiB perl-IO-Socket-IP noarch 0.43-1.fc42 fedora 100.3 KiB perl-IO-Socket-SSL noarch 2.089-1.fc42 fedora 703.3 KiB perl-IPC-Open3 noarch 1.22-512.fc42 fedora 22.5 KiB perl-MIME-Base32 noarch 1.303-21.fc41 fedora 30.7 KiB perl-MIME-Base64 aarch64 3.16-511.fc41 fedora 222.2 KiB perl-Net-SSLeay aarch64 1.94-7.fc41 fedora 1.4 MiB perl-POSIX aarch64 2.20-512.fc42 fedora 327.3 KiB perl-PathTools aarch64 3.91-511.fc41 fedora 352.1 KiB perl-Pod-Escapes noarch 1:1.07-511.fc41 fedora 24.9 KiB perl-Pod-Perldoc noarch 3.28.01-512.fc41 fedora 163.7 KiB perl-Pod-Simple noarch 1:3.45-511.fc41 fedora 560.9 KiB perl-Pod-Usage noarch 4:2.03-511.fc41 fedora 84.8 KiB perl-Scalar-List-Utils aarch64 5:1.68-1.fc42 fedora 281.0 KiB perl-SelectSaver noarch 1.02-512.fc42 fedora 2.2 KiB perl-Socket aarch64 4:2.038-511.fc41 fedora 272.1 KiB perl-Storable aarch64 1:3.32-511.fc41 fedora 372.5 KiB perl-Symbol noarch 1.09-512.fc42 fedora 6.8 KiB perl-Term-ANSIColor noarch 5.01-512.fc41 fedora 97.5 KiB perl-Term-Cap noarch 1.18-511.fc41 fedora 29.3 KiB perl-Test-Harness noarch 1:3.50-1.fc42 fedora 559.6 KiB perl-Text-ParseWords noarch 3.31-511.fc41 fedora 13.6 KiB perl-Text-Tabs+Wrap noarch 2024.001-511.fc41 fedora 22.6 KiB perl-Thread-Queue noarch 3.14-511.fc41 fedora 28.9 KiB perl-Time-Local noarch 2:1.350-511.fc41 fedora 69.0 KiB perl-URI noarch 5.31-1.fc42 fedora 257.0 KiB perl-base noarch 2.27-512.fc42 fedora 12.5 KiB perl-constant noarch 1.33-512.fc41 fedora 26.2 KiB perl-devel aarch64 4:5.40.0-512.fc42 fedora 8.0 MiB perl-if noarch 0.61.000-512.fc42 fedora 5.8 KiB perl-lib aarch64 0.65-512.fc42 fedora 8.5 KiB perl-libnet noarch 3.15-512.fc41 fedora 289.4 KiB perl-libs aarch64 4:5.40.0-512.fc42 fedora 10.9 MiB perl-locale noarch 1.12-512.fc42 fedora 6.5 KiB perl-mro aarch64 1.29-512.fc42 fedora 209.7 KiB perl-overload noarch 1.37-512.fc42 fedora 71.5 KiB perl-overloading noarch 0.02-512.fc42 fedora 4.8 KiB perl-parent noarch 1:0.243-1.fc42 fedora 10.2 KiB perl-podlators noarch 1:6.0.2-2.fc41 fedora 317.5 KiB perl-threads aarch64 1:2.40-511.fc41 fedora 263.2 KiB perl-threads-shared aarch64 1.69-511.fc41 fedora 231.8 KiB perl-vars noarch 1.05-512.fc42 fedora 3.9 KiB perl-version aarch64 9:0.99.33-1.fc42 fedora 288.9 KiB python-pip-wheel noarch 24.3.1-1.fc42 fedora 1.2 MiB python3 aarch64 3.13.0-1.fc42 fedora 211.8 KiB python3-libs aarch64 3.13.0-1.fc42 fedora 49.7 MiB python3-pyparsing noarch 3.1.2-7.fc41 fedora 1.0 MiB systemtap-sdt-devel aarch64 5.2-1.fc42 fedora 182.4 KiB systemtap-sdt-dtrace aarch64 5.2-1.fc42 fedora 179.0 KiB tzdata noarch 2024a-9.fc41 fedora 1.7 MiB Transaction Summary: Installing: 114 packages Total size of inbound packages is 75 MiB. Need to download 7 MiB. After this operation, 259 MiB extra will be used (install 259 MiB, remove 0 B). [1/1] gcc-0:14.2.1-6.fc42.aarch64 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-1:4.4.1-9.fc42.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [2/7] perl-File-Temp-1:0.231.100-511.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [3/9] perl-Getopt-Long-1:2.58-2.fc41.no 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 4/10] perl-interpreter-4:5.40.0-512.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 5/11] zlib-ng-compat-devel-0:2.2.2-1. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 6/12] cpp-0:14.2.1-6.fc42.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 7/13] glibc-devel-0:2.40.9000-21.fc42 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 8/14] libasan-0:14.2.1-6.fc42.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 9/15] 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| 00m00s [ 95/116] Installing perl-ExtUtils-Inst 100% | 85.1 MiB/s | 87.2 KiB | 00m00s [ 96/116] Installing perl-ExtUtils-Make 100% | 181.8 MiB/s | 744.8 KiB | 00m00s [ 97/116] Installing systemtap-sdt-deve 100% | 59.9 MiB/s | 183.9 KiB | 00m00s [ 98/116] Installing kernel-headers-0:6 100% | 148.4 MiB/s | 6.5 MiB | 00m00s [ 99/116] Installing libxcrypt-devel-0: 100% | 10.7 MiB/s | 32.9 KiB | 00m00s [100/116] Installing glibc-devel-0:2.40 100% | 120.5 MiB/s | 2.3 MiB | 00m00s [101/116] Installing perl-devel-4:5.40. 100% | 447.4 MiB/s | 8.1 MiB | 00m00s [102/116] Installing cmake-filesystem-0 100% | 3.7 MiB/s | 7.6 KiB | 00m00s [103/116] Installing gsl-0:2.7.1-11.fc4 100% | 340.6 MiB/s | 3.7 MiB | 00m00s [104/116] Installing libubsan-0:14.2.1- 100% | 232.5 MiB/s | 476.1 KiB | 00m00s [105/116] Installing libatomic-0:14.2.1 100% | 68.2 MiB/s | 69.8 KiB | 00m00s [106/116] Installing libasan-0:14.2.1-6 100% | 308.0 MiB/s | 1.5 MiB | 00m00s [107/116] Installing make-1:4.4.1-9.fc4 100% | 231.4 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Finish: build setup for bcftools-1.15.1-10.fc42.src.rpm Start: rpmbuild bcftools-1.15.1-10.fc42.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721174400 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.SnpKM1 + 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.GzOqHr + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + cd /builddir/build/BUILD/bcftools-1.15.1-build + rm -rf bcftools-1.15.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/bcftools-1.15.1.tar.bz2 + STATUS=0 + '[' 0 -ne 0 ']' + cd bcftools-1.15.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (bcftools-1.15.1-aarch64-fix-vcf_plugin-tests.patch):' Patch #0 (bcftools-1.15.1-aarch64-fix-vcf_plugin-tests.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file plugins/fill-tags.c + sed -i '1s|/usr/bin/env perl|/usr/bin/perl|' misc/color-chrs.pl misc/demo-flt.pl misc/run-roh.pl misc/vcfutils.pl misc/plot-vcfstats + sed -i '1s|/usr/bin/env python3\{0,1\}|/usr/bin/python3|' misc/gff2gff.py misc/guess-ploidy.py misc/plot-roh.py + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.BWYFgq + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bcftools-1.15.1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./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 2024-12-07 04:48:46.399233073 +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* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=aarch64-redhat-linux --host=aarch64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --with-htslib=system --enable-perl-filters --enable-libgsl '--with-bcf-plugin-path=/usr/local/libexec/bcftools:$(plugindir)' checking for aarch64-redhat-linux-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for gsl/gsl_version.h... yes checking for library containing cblas_dgemm... -lgslcblas checking for gsl_multifit_gradient in -lgsl... yes checking for library containing Perl_call_pv... -lperl checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h configure: License has been changed to GPL. Linking against the GNU scientific library requires that the resulting binary is licensed using the GNU General Public License. In particular, this means you will have to follow the terms of this license in order to distribute binary copies. For more information see the INSTALL file. Text of the GNU General Public License can be found in the LICENSE file, or at http://www.gnu.org/copyleft/gpl.html Information on the GNU Scientific Library, including the rationale for its choice of license can be found at https://www.gnu.org/software/gsl/ + /usr/bin/make -O -j4 V=1 VERBOSE=1 echo '#define BCFTOOLS_VERSION "1.15.1"' > version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o tabix.o tabix.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfindex.o vcfindex.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfisec.o vcfisec.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfquery.o vcfquery.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcffilter.o vcffilter.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfstats.o vcfstats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfsom.o vcfsom.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfgtcheck.o vcfgtcheck.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfview.o vcfview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfmerge.o vcfmerge.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfnorm.o vcfnorm.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfroh.o vcfroh.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfconcat.o vcfconcat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -c -o filter.o filter.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcmp.o vcmp.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o gvcf.o gvcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfcall.o vcfcall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o mcall.o mcall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfannotate.o vcfannotate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o reheader.o reheader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o tsv2vcf.o tsv2vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfhead.o vcfhead.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o HMM.o HMM.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfcnv.o vcfcnv.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfconvert.o vcfconvert.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o convert.o convert.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o bin.o bin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o ploidy.o ploidy.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o version.o version.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o consensus.o consensus.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o hclust.o hclust.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o smpl_ilist.o smpl_ilist.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfbuf.o vcfbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o mpileup.o mpileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o bam2bcf.o bam2bcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o cols.o cols.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security 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-Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o em.o em.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o ccall.o ccall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o kmin.o kmin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o str_finder.o str_finder.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o prob1.o prob1.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o abuf.o abuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o polysomy.o polysomy.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DPLUGINPATH='"/usr/local/libexec/bcftools:/usr/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall 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-specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o csq.o csq.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 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-Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DUSE_GPL -c -o main.o main.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/test-rbuf test/test-rbuf.o -lz gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o polysomy.o peakfit.o vcfplugin.o -lhts -lm -lz -lgsl -lgslcblas -Wl,--enable-new-dtags -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -fstack-protector-strong -L/usr/local/lib -L/usr/lib64/perl5/CORE -lperl -lpthread -lresolv -ldl -lm -lcrypt -lutil -lc -lpthread + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.i3pyZp + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + '[' /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT ++ dirname /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT + mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build + mkdir /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bcftools-1.15.1 + /usr/bin/make install DESTDIR=/builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/bin /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/man/man1 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/libexec/bcftools /usr/bin/install -p bcftools /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/bin /usr/bin/install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/bin /usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/man/man1 /usr/bin/install -p plugins/*.so /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/libexec/bcftools + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.15.1-10.fc42 --unique-debug-suffix -1.15.1-10.fc42.aarch64 --unique-debug-src-base bcftools-1.15.1-10.fc42.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1 find-debuginfo: starting Extracting debug info from 39 files DWARF-compressing 39 files sepdebugcrcfix: Updated 39 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/bcftools-1.15.1-10.fc42.aarch64 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.roVyqv + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bcftools-1.15.1 + ldd bcftools + grep -E '/lib(64)?/libhts\.so\.' libhts.so.3 => /lib64/libhts.so.3 (0x0000ffffbb920000) + make test ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} ./test/test.pl: module IO::Pty not found; skipping usage tests test_usage: bcftools test_tabix: tabix /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/15b4MR0Ox_/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/15b4MR0Ox_/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/15b4MR0Ox_/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/15b4MR0Ox_/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/15b4MR0Ox_/idx.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/15b4MR0Ox_/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/15b4MR0Ox_/idx.bcf.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/15b4MR0Ox_/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/15b4MR0Ox_/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/15b4MR0Ox_/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/15b4MR0Ox_/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/15b4MR0Ox_/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/15b4MR0Ox_/empty.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/15b4MR0Ox_/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/15b4MR0Ox_/empty.bcf.csi .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s - /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/check.1.chk /tmp/15b4MR0Ox_/check.2.chk /tmp/15b4MR0Ox_/check.3.chk /tmp/15b4MR0Ox_/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/15b4MR0Ox_/stats.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/stats.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/isec.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec.tab.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec.tab.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec-miss.1.1.vcf.gz /tmp/15b4MR0Ox_/isec-miss.1.2.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec-miss.1.1.vcf.gz /tmp/15b4MR0Ox_/isec-miss.1.2.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec-miss.1.1.vcf.gz /tmp/15b4MR0Ox_/isec-miss.1.2.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec-miss.1.1.vcf.gz /tmp/15b4MR0Ox_/isec-miss.1.2.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec-miss.2.1.vcf.gz /tmp/15b4MR0Ox_/isec-miss.2.2.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec-miss.2.1.vcf.gz /tmp/15b4MR0Ox_/isec-miss.2.2.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec-miss.2.1.vcf.gz /tmp/15b4MR0Ox_/isec-miss.2.2.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/isec-miss.2.1.vcf.gz /tmp/15b4MR0Ox_/isec-miss.2.2.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.join.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.join.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.join.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.join.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.vcf.gz /tmp/15b4MR0Ox_/merge.LPL.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.vcf.gz /tmp/15b4MR0Ox_/merge.LPL.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.bcf /tmp/15b4MR0Ox_/merge.LPL.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.bcf /tmp/15b4MR0Ox_/merge.LPL.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.vcf.gz /tmp/15b4MR0Ox_/merge.LPL.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.vcf.gz /tmp/15b4MR0Ox_/merge.LPL.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.bcf /tmp/15b4MR0Ox_/merge.LPL.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.bcf /tmp/15b4MR0Ox_/merge.LPL.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.vcf.gz /tmp/15b4MR0Ox_/merge.LPL.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.vcf.gz /tmp/15b4MR0Ox_/merge.LPL.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.bcf /tmp/15b4MR0Ox_/merge.LPL.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.bcf /tmp/15b4MR0Ox_/merge.LPL.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.vcf.gz /tmp/15b4MR0Ox_/merge.LPL.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.vcf.gz /tmp/15b4MR0Ox_/merge.LPL.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.bcf /tmp/15b4MR0Ox_/merge.LPL.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.bcf /tmp/15b4MR0Ox_/merge.LPL.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.vcf.gz /tmp/15b4MR0Ox_/merge.LPL.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.vcf.gz /tmp/15b4MR0Ox_/merge.LPL.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.bcf /tmp/15b4MR0Ox_/merge.LPL.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.bcf /tmp/15b4MR0Ox_/merge.LPL.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.vcf.gz /tmp/15b4MR0Ox_/merge.LPL.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.vcf.gz /tmp/15b4MR0Ox_/merge.LPL.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.bcf /tmp/15b4MR0Ox_/merge.LPL.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.LPL.a.bcf /tmp/15b4MR0Ox_/merge.LPL.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.a.vcf.gz /tmp/15b4MR0Ox_/merge.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.a.vcf.gz /tmp/15b4MR0Ox_/merge.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.a.bcf /tmp/15b4MR0Ox_/merge.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.a.bcf /tmp/15b4MR0Ox_/merge.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.a.vcf.gz /tmp/15b4MR0Ox_/merge.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.a.vcf.gz /tmp/15b4MR0Ox_/merge.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.a.bcf /tmp/15b4MR0Ox_/merge.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.a.bcf /tmp/15b4MR0Ox_/merge.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.a.vcf.gz /tmp/15b4MR0Ox_/merge.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.a.vcf.gz /tmp/15b4MR0Ox_/merge.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.a.bcf /tmp/15b4MR0Ox_/merge.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.a.bcf /tmp/15b4MR0Ox_/merge.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.2.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.2.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.2.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.2.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.2.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.2.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.2.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.2.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.2.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.2.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.2.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.2.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.3.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.3.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.3.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.3.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.4.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.4.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.4.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.4.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gvcf.merge.1.vcf.gz /tmp/15b4MR0Ox_/gvcf.merge.2.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gvcf.merge.1.vcf.gz /tmp/15b4MR0Ox_/gvcf.merge.2.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gvcf.merge.1.bcf /tmp/15b4MR0Ox_/gvcf.merge.2.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gvcf.merge.1.bcf /tmp/15b4MR0Ox_/gvcf.merge.2.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.2.a.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.2.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.2.a.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.2.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.3.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.3.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.4.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.4.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.4.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.4.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.5.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.5.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.5.a.bcf /tmp/15b4MR0Ox_/merge.5.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/15b4MR0Ox_/merge.5.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.6.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.6.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.6.a.bcf /tmp/15b4MR0Ox_/merge.6.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/15b4MR0Ox_/merge.6.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.7.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.7.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.7.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.7.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.8.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.8.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.8.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.8.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.7.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.7.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.7.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.7.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9b.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9c.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9b.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9c.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.bcf /tmp/15b4MR0Ox_/merge.gvcf.9b.bcf /tmp/15b4MR0Ox_/merge.gvcf.9c.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.bcf /tmp/15b4MR0Ox_/merge.gvcf.9b.bcf /tmp/15b4MR0Ox_/merge.gvcf.9c.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9b.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9c.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9b.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9c.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.bcf /tmp/15b4MR0Ox_/merge.gvcf.9b.bcf /tmp/15b4MR0Ox_/merge.gvcf.9c.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.bcf /tmp/15b4MR0Ox_/merge.gvcf.9b.bcf /tmp/15b4MR0Ox_/merge.gvcf.9c.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9b.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9c.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9d.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9b.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9c.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9d.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.bcf /tmp/15b4MR0Ox_/merge.gvcf.9b.bcf /tmp/15b4MR0Ox_/merge.gvcf.9c.bcf /tmp/15b4MR0Ox_/merge.gvcf.9d.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.bcf /tmp/15b4MR0Ox_/merge.gvcf.9b.bcf /tmp/15b4MR0Ox_/merge.gvcf.9c.bcf /tmp/15b4MR0Ox_/merge.gvcf.9d.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9b.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9c.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9d.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9b.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9c.vcf.gz /tmp/15b4MR0Ox_/merge.gvcf.9d.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.bcf /tmp/15b4MR0Ox_/merge.gvcf.9b.bcf /tmp/15b4MR0Ox_/merge.gvcf.9c.bcf /tmp/15b4MR0Ox_/merge.gvcf.9d.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.9a.bcf /tmp/15b4MR0Ox_/merge.gvcf.9b.bcf /tmp/15b4MR0Ox_/merge.gvcf.9c.bcf /tmp/15b4MR0Ox_/merge.gvcf.9d.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.gvcf.10.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.noidx.a.vcf.gz /tmp/15b4MR0Ox_/merge.noidx.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.noidx.a.vcf.gz /tmp/15b4MR0Ox_/merge.noidx.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.noidx.a.bcf /tmp/15b4MR0Ox_/merge.noidx.b.bcf /tmp/15b4MR0Ox_/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/15b4MR0Ox_/merge.noidx.a.bcf /tmp/15b4MR0Ox_/merge.noidx.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.noidx.a.bcf /tmp/15b4MR0Ox_/merge.noidx.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.noidx.a.bcf /tmp/15b4MR0Ox_/merge.noidx.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.8.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.8.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.8.a.bcf /tmp/15b4MR0Ox_/merge.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/15b4MR0Ox_/merge.8.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.8.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.8.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.8.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.8.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.9.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.9.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.9.a.bcf /tmp/15b4MR0Ox_/merge.9.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/15b4MR0Ox_/merge.9.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.9.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.9.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.9.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/merge.9.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.variantkey.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.vectors.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/view.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -p /tmp/15b4MR0Ox_/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/15b4MR0Ox_/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -P /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -GVsnps /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/regions.tab.gz /tmp/15b4MR0Ox_/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/regions.tab.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/regions.bed /tmp/15b4MR0Ox_/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/regions.bed /tmp/15b4MR0Ox_/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/15b4MR0Ox_/regions.bed.gz /tmp/15b4MR0Ox_/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/regions.bed.gz /tmp/15b4MR0Ox_/regions.vcf.gz .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots4.vcf.gz -c +INFO /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots4.vcf.gz -c +INFO /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots11.vcf.gz -c FMT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots11.vcf.gz -c FMT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c FMT/newGT:=GT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots2.vcf.gz -c FMT/newGT:=GT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots12.vcf.gz -c FMT/GT:=newGT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots12.vcf.gz -c FMT/GT:=newGT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annotate20.src.vcf.gz -c FMT/GT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annotate20.src.vcf.gz -c FMT/GT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annotate20.src.vcf.gz -c +FMT/GT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annotate20.src.vcf.gz -c +FMT/GT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annotate20.src.vcf.gz -c -FMT/GT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annotate20.src.vcf.gz -c -FMT/GT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/annotate24.src.vcf.gz -c XX /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annotate24.src.vcf.gz -c XX /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/annots.id.vcf.gz -c ALT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots.id.vcf.gz -c ALT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots.id.vcf.gz -c +ALT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/annots.id.vcf.gz -c +ALT /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/plugin1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -i /tmp/15b4MR0Ox_/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/15b4MR0Ox_/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -i /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/split.1.1 && cd /tmp/15b4MR0Ox_/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/15b4MR0Ox_/split.1.2 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.2.txt && cd /tmp/15b4MR0Ox_/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/15b4MR0Ox_/split.1.3 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.3.txt && cd /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/split.1.7 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.grp.1.1.txt && cd /tmp/15b4MR0Ox_/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/15b4MR0Ox_/split.2.1 && cd /tmp/15b4MR0Ox_/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/15b4MR0Ox_/scatter.1.1 -n 3 && cd /tmp/15b4MR0Ox_/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/15b4MR0Ox_/scatter.1.2 -s 21,22 && cd /tmp/15b4MR0Ox_/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/15b4MR0Ox_/scatter.1.3 -s 21,22 -x X && cd /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.1.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.1.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.1.a.bcf /tmp/15b4MR0Ox_/concat.1.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob /tmp/15b4MR0Ox_/concat.1.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.2.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.2.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.2.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.2.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.2.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.2.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.2.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.2.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.3.a.vcf.gz /tmp/15b4MR0Ox_/concat.3.b.vcf.gz /tmp/15b4MR0Ox_/concat.3.0.vcf.gz /tmp/15b4MR0Ox_/concat.3.c.vcf.gz /tmp/15b4MR0Ox_/concat.3.d.vcf.gz /tmp/15b4MR0Ox_/concat.3.e.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.3.a.vcf.gz /tmp/15b4MR0Ox_/concat.3.b.vcf.gz /tmp/15b4MR0Ox_/concat.3.0.vcf.gz /tmp/15b4MR0Ox_/concat.3.c.vcf.gz /tmp/15b4MR0Ox_/concat.3.d.vcf.gz /tmp/15b4MR0Ox_/concat.3.e.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.3.a.bcf /tmp/15b4MR0Ox_/concat.3.b.bcf /tmp/15b4MR0Ox_/concat.3.0.bcf /tmp/15b4MR0Ox_/concat.3.c.bcf /tmp/15b4MR0Ox_/concat.3.d.bcf /tmp/15b4MR0Ox_/concat.3.e.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.3.a.bcf /tmp/15b4MR0Ox_/concat.3.b.bcf /tmp/15b4MR0Ox_/concat.3.0.bcf /tmp/15b4MR0Ox_/concat.3.c.bcf /tmp/15b4MR0Ox_/concat.3.d.bcf /tmp/15b4MR0Ox_/concat.3.e.bcf /tmp/15b4MR0Ox_/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: 1179020238 .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --naive-force /tmp/15b4MR0Ox_/naive_concat.0.bcf /tmp/15b4MR0Ox_/naive_concat.1.bcf /tmp/15b4MR0Ox_/naive_concat.2.bcf /tmp/15b4MR0Ox_/naive_concat.3.bcf /tmp/15b4MR0Ox_/naive_concat.4.bcf /tmp/15b4MR0Ox_/naive_concat.5.bcf /tmp/15b4MR0Ox_/naive_concat.6.bcf /tmp/15b4MR0Ox_/naive_concat.7.bcf /tmp/15b4MR0Ox_/naive_concat.8.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/naive_concat.0.vcf.gz /tmp/15b4MR0Ox_/naive_concat.1.vcf.gz /tmp/15b4MR0Ox_/naive_concat.2.vcf.gz /tmp/15b4MR0Ox_/naive_concat.3.vcf.gz /tmp/15b4MR0Ox_/naive_concat.4.vcf.gz /tmp/15b4MR0Ox_/naive_concat.5.vcf.gz /tmp/15b4MR0Ox_/naive_concat.6.vcf.gz /tmp/15b4MR0Ox_/naive_concat.7.vcf.gz /tmp/15b4MR0Ox_/naive_concat.8.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.4.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.4.a.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.4.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.4.a.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.5.a.vcf.gz /tmp/15b4MR0Ox_/concat.5.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.5.a.vcf.gz /tmp/15b4MR0Ox_/concat.5.b.vcf.gz /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.5.a.bcf /tmp/15b4MR0Ox_/concat.5.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.5.a.bcf /tmp/15b4MR0Ox_/concat.5.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.5.a.bcf /tmp/15b4MR0Ox_/concat.5.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/concat.5.a.bcf /tmp/15b4MR0Ox_/concat.5.b.bcf /tmp/15b4MR0Ox_/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/15b4MR0Ox_/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/empty.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/rename.map -Ov /tmp/15b4MR0Ox_/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/15b4MR0Ox_/rename.map -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --tag PL /tmp/15b4MR0Ox_/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/consensus.1.chain.new >/dev/null; cat /tmp/15b4MR0Ox_/consensus.1.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/consensus.2.chain.new >/dev/null; cat /tmp/15b4MR0Ox_/consensus.2.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/consensus.3.chain.new >/dev/null; cat /tmp/15b4MR0Ox_/consensus.3.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/15b4MR0Ox_/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/15b4MR0Ox_/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H 1 -c /tmp/15b4MR0Ox_/consensus.4.chain.new >/dev/null; cat /tmp/15b4MR0Ox_/consensus.4.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.1.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.1.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.1.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.1.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.1.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.1.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.2.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.1.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.1.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.1.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.1.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.1.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.1.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.1.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.ntop.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.ntop.vcf.gz -g /tmp/15b4MR0Ox_/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/15b4MR0Ox_/gtcheck.5.vcf.gz -g /tmp/15b4MR0Ox_/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok Number of tests: total .. 1725 passed .. 1725 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: bcftools-1.15.1-10.fc42.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.WFKdaw + 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.18jNax + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + cd bcftools-1.15.1 + LICENSEDIR=/builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/licenses/bcftools + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/licenses/bcftools + cp -pr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/LICENSE /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/licenses/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Provides: bcftools = 1.15.1-10.fc42 bcftools(aarch-64) = 1.15.1-10.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl /usr/bin/python3 ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgsl.so.27()(64bit) libgslcblas.so.0()(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libperl.so.5.40()(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Conflicts: samtools < 1.0 Processing files: bcftools-debugsource-1.15.1-10.fc42.aarch64 Provides: bcftools-debugsource = 1.15.1-10.fc42 bcftools-debugsource(aarch-64) = 1.15.1-10.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bcftools-debuginfo-1.15.1-10.fc42.aarch64 Provides: bcftools-debuginfo = 1.15.1-10.fc42 bcftools-debuginfo(aarch-64) = 1.15.1-10.fc42 debuginfo(build-id) = 0b85ba897eef55ece959bfd1aae6b2ab451e6831 debuginfo(build-id) = 117546edb10aa5af0e85d29a9b727ee18950f71f debuginfo(build-id) = 2cbbbf55b7236e8728c5b8707b07da60a943ac3f debuginfo(build-id) = 4986e2d40df7c5aa1eee3d44fbdc8f29e7228411 debuginfo(build-id) = 4b23e6e294dd30d7a4ec81bd6661a8ecd0b29e17 debuginfo(build-id) = 4b8ff90610bde0e45375cc9e302db704e0bb2421 debuginfo(build-id) = 4cc2519f30627a8f39176d7498b739caa9535d86 debuginfo(build-id) = 559c3652cd2dde623c84db6e43041c8419e869f0 debuginfo(build-id) = 5adb940f471f29c8280e061384aa604d7ef157c2 debuginfo(build-id) = 5c2e4c83decd6d3ef81b5499e6c0d7934992d5ba debuginfo(build-id) = 65af0d3ed626e727d6a255a247298b1905f23a7e debuginfo(build-id) = 680813332bf6f161f08b8732adabfa7332d66123 debuginfo(build-id) = 6b7c85fc5cb9ab26c4a15edd9f78b677c8706379 debuginfo(build-id) = 6f64932f3c4d8c458ff43a36f69eacfd66877a4a debuginfo(build-id) = 709061bf9e9fb29d36eb53b54faa60fd092c8790 debuginfo(build-id) = 774c4716eb30b80c5dfda80c96c9156df4b91a1d debuginfo(build-id) = 7fc8e589b7d47e5baa8e3f86ef179066245ba5d9 debuginfo(build-id) = 8311d42a05ffd7a628bff404887459254898d65d debuginfo(build-id) = 83fdc53f314ef4511cc67268d3572cec6dab02ea debuginfo(build-id) = 860dc5af0b9d7afa07a74cde891c947d437cd1ef debuginfo(build-id) = 8f260a5e8957ff26d0226c85f8a07598d2890757 debuginfo(build-id) = 9288b349c40bbef9fd00729906f59afb82315427 debuginfo(build-id) = 92c8f8b47c40fdc7145d1833f727105a304e831f debuginfo(build-id) = 94102da909e2d3efa095169e1752130c0fbdf766 debuginfo(build-id) = 971a3ae261dfd508c85b031fd393cdad2049b044 debuginfo(build-id) = 97610653565849f1e086f73133479aa1edea9833 debuginfo(build-id) = a2b449776f3c1591c2d627b3c662fffc188f0df5 debuginfo(build-id) = a96bbe372f9e42f30a64ff7f7061f3e9c866f4b5 debuginfo(build-id) = bc25135da4ceb5348b112b3f770fe62cf5c12a0d debuginfo(build-id) = bfe303e45b9e2242069d65f59afc79b8c52b25b4 debuginfo(build-id) = c2f22d4ef7583fa7701cdac23a3592de2e6fdb4b debuginfo(build-id) = ce46c15da56ce42c27463feedb1f9b7fc1dd5af7 debuginfo(build-id) = d0000ffa4c21f70037db966fa3c234ac7f39f4db debuginfo(build-id) = d20fb8ae28338bb43e08a1e75eb8103b473b30bf debuginfo(build-id) = d3f8d7d67ca92e83597253d8a4e49dd5bc53232c debuginfo(build-id) = dc27639c0eb290da8ad58064a28c930fb22e17aa debuginfo(build-id) = e396ecc5d47b18e2aa0ec997cdebef21b590fd1a debuginfo(build-id) = e6ffcaa9d7c0b0c45d88fd6460fe6080435f2213 debuginfo(build-id) = fe357d906cc2edb61ed8287784b23a24db333359 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bcftools-debugsource(aarch-64) = 1.15.1-10.fc42 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT Wrote: /builddir/build/RPMS/bcftools-1.15.1-10.fc42.aarch64.rpm Wrote: /builddir/build/RPMS/bcftools-debugsource-1.15.1-10.fc42.aarch64.rpm Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.15.1-10.fc42.aarch64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.bBH6QO + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + test -d /builddir/build/BUILD/bcftools-1.15.1-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/bcftools-1.15.1-build + rm -rf /builddir/build/BUILD/bcftools-1.15.1-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild bcftools-1.15.1-10.fc42.src.rpm Finish: build phase for bcftools-1.15.1-10.fc42.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-aarch64-1733546906.841703/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-1.15.1-10.fc42.src.rpm) Config(child) 1 minutes 7 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-debugsource", "epoch": null, "version": "1.15.1", "release": "10.fc42", "arch": "aarch64" }, { "name": "bcftools-debuginfo", "epoch": null, "version": "1.15.1", "release": "10.fc42", "arch": "aarch64" }, { "name": "bcftools", "epoch": null, "version": "1.15.1", "release": "10.fc42", "arch": "src" }, { "name": "bcftools", "epoch": null, "version": "1.15.1", "release": "10.fc42", "arch": "aarch64" } ] } RPMResults finished