Warning: Permanently added '98.81.246.55' (ED25519) to the list of known hosts. Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-b4_0l74n/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-b4_0l74n/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769508937.072208 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.6 starting (python version = 3.14.2, NVR = mock-6.6-1.fc43), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-b4_0l74n/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-b4_0l74n/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769508937.072208 -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-b4_0l74n/bcftools/bcftools.spec) Config(rhel+epel-9-aarch64) Start: clean chroot Finish: clean chroot Mock Version: 6.6 INFO: Mock Version: 6.6 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-aarch64-bootstrap-1769508937.072208/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using container image: registry.access.redhat.com/ubi9/ubi INFO: Pulling image: registry.access.redhat.com/ubi9/ubi INFO: Tagging container image as mock-bootstrap-45f1f5a7-ca32-423d-ad4d-78f47808e874 INFO: Checking that 150f16ae1250906effaf34690ffd1988f54abd0ab77f7881ec6612c1694cca52 image matches host's architecture INFO: Copy content of container 150f16ae1250906effaf34690ffd1988f54abd0ab77f7881ec6612c1694cca52 to /var/lib/mock/rhel+epel-9-aarch64-bootstrap-1769508937.072208/root INFO: mounting 150f16ae1250906effaf34690ffd1988f54abd0ab77f7881ec6612c1694cca52 with podman image mount INFO: image 150f16ae1250906effaf34690ffd1988f54abd0ab77f7881ec6612c1694cca52 as /var/lib/containers/storage/overlay/aa0c4cb11dd3d609311bf6e8aa39e65c9d31249a218dc5e25945e162e8ed3773/merged INFO: umounting image 150f16ae1250906effaf34690ffd1988f54abd0ab77f7881ec6612c1694cca52 (/var/lib/containers/storage/overlay/aa0c4cb11dd3d609311bf6e8aa39e65c9d31249a218dc5e25945e162e8ed3773/merged) with podman image umount INFO: Removing image mock-bootstrap-45f1f5a7-ca32-423d-ad4d-78f47808e874 INFO: Package manager dnf4 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/rhel+epel-9-aarch64-1769508937.072208/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 dnf4 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.16.1.3-39.el9.aarch64 python3-dnf-4.14.0-31.el9.noarch python3-dnf-plugins-core-4.3.0-24.el9_7.noarch yum-4.14.0-31.el9.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 115 kB/s | 4.8 kB 00:00 Red Hat Enterprise Linux - BaseOS 143 MB/s | 120 MB 00:00 Red Hat Enterprise Linux - AppStream 115 MB/s | 88 MB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 32 MB/s | 12 MB 00:00 Extra Packages for Enterprise Linux 9 - aarch64 39 MB/s | 20 MB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: bash aarch64 5.1.8-9.el9 baseos 1.7 M bzip2 aarch64 1.0.8-10.el9_5 baseos 59 k coreutils aarch64 8.32-39.el9 baseos 1.1 M cpio aarch64 2.13-16.el9 baseos 278 k diffutils aarch64 3.7-12.el9 baseos 396 k epel-rpm-macros noarch 9-17.el9 epel 15 k findutils aarch64 1:4.8.0-7.el9 baseos 552 k gawk aarch64 5.1.0-6.el9 baseos 1.0 M glibc-minimal-langpack aarch64 2.34-231.el9_7.2 baseos 22 k grep aarch64 3.6-5.el9 baseos 270 k gzip aarch64 1.12-1.el9 baseos 166 k info aarch64 6.7-15.el9 baseos 225 k patch aarch64 2.7.6-16.el9 appstream 126 k redhat-release aarch64 9.7-0.7.el9 baseos 53 k redhat-rpm-config noarch 210-1.el9 appstream 70 k rpm-build aarch64 4.16.1.3-39.el9 appstream 66 k sed aarch64 4.8-9.el9 baseos 307 k tar aarch64 2:1.34-9.el9_7 baseos 877 k unzip aarch64 6.0-59.el9 baseos 178 k util-linux aarch64 2.37.4-21.el9 baseos 2.3 M which aarch64 2.21-30.el9_6 baseos 41 k xz aarch64 5.2.5-8.el9_0 baseos 230 k Installing dependencies: alternatives aarch64 1.24-2.el9 baseos 41 k ansible-srpm-macros noarch 1-16.el9 epel 21 k audit-libs aarch64 3.1.5-7.el9 baseos 117 k basesystem noarch 11-13.el9 baseos 8.0 k binutils aarch64 2.35.2-67.el9_7.1 baseos 4.8 M binutils-gold aarch64 2.35.2-67.el9_7.1 baseos 881 k bzip2-libs aarch64 1.0.8-10.el9_5 baseos 43 k ca-certificates noarch 2025.2.80_v9.0.305-91.el9 baseos 1.0 M coreutils-common aarch64 8.32-39.el9 baseos 2.0 M cracklib aarch64 2.9.6-27.el9 baseos 99 k cracklib-dicts aarch64 2.9.6-27.el9 baseos 3.6 M crypto-policies noarch 20250905-1.git377cc42.el9_7 baseos 90 k curl aarch64 7.76.1-34.el9 baseos 289 k cyrus-sasl-lib aarch64 2.1.27-22.el9 baseos 754 k debugedit aarch64 5.0-11.el9 appstream 77 k dwz aarch64 0.16-1.el9 appstream 134 k ed aarch64 1.14.2-12.el9 baseos 77 k efi-srpm-macros noarch 6-4.el9 appstream 21 k elfutils aarch64 0.193-1.el9 baseos 568 k elfutils-debuginfod-client aarch64 0.193-1.el9 baseos 43 k elfutils-default-yama-scope noarch 0.193-1.el9 baseos 9.7 k elfutils-libelf aarch64 0.193-1.el9 baseos 204 k elfutils-libs aarch64 0.193-1.el9 baseos 265 k file aarch64 5.39-16.el9 baseos 52 k file-libs aarch64 5.39-16.el9 baseos 591 k filesystem aarch64 3.16-5.el9 baseos 4.8 M fonts-srpm-macros noarch 1:2.0.5-7.el9.1 appstream 29 k forge-srpm-macros noarch 0.4.0-1.el9 epel 19 k fpc-srpm-macros noarch 1.3-7.el9 epel 7.5 k gdb-minimal aarch64 16.3-2.el9 appstream 4.2 M gdbm-libs aarch64 1:1.23-1.el9 baseos 59 k ghc-srpm-macros noarch 1.5.0-6.el9 appstream 9.0 k ghc-srpm-macros-epel noarch 1.9.1-1.el9 epel 7.5 k glibc aarch64 2.34-231.el9_7.2 baseos 1.7 M glibc-common aarch64 2.34-231.el9_7.2 baseos 297 k glibc-gconv-extra aarch64 2.34-231.el9_7.2 baseos 1.7 M gmp aarch64 1:6.2.0-13.el9 baseos 269 k go-srpm-macros noarch 3.6.0-12.el9_7 appstream 27 k go-srpm-macros-epel noarch 3.8.0-1.el9 epel 26 k groff-base aarch64 1.22.4-10.el9 baseos 1.0 M json-c aarch64 0.14-11.el9 baseos 44 k kernel-srpm-macros noarch 1.0-14.el9 appstream 14 k keyutils-libs aarch64 1.6.3-1.el9 baseos 34 k krb5-libs aarch64 1.21.1-8.el9_6 baseos 769 k libacl aarch64 2.3.1-4.el9 baseos 24 k libarchive aarch64 3.5.3-6.el9_6 baseos 385 k libattr aarch64 2.5.1-3.el9 baseos 20 k libblkid aarch64 2.37.4-21.el9 baseos 109 k libbrotli aarch64 1.0.9-7.el9_5 baseos 315 k libcap aarch64 2.48-10.el9 baseos 70 k libcap-ng aarch64 0.8.2-7.el9 baseos 35 k libcom_err aarch64 1.46.5-8.el9 baseos 26 k libcurl aarch64 7.76.1-34.el9 baseos 278 k libdb aarch64 5.3.28-57.el9_6 baseos 710 k libeconf aarch64 0.4.1-4.el9 baseos 29 k libevent aarch64 2.1.12-8.el9_4 baseos 260 k libfdisk aarch64 2.37.4-21.el9 baseos 150 k libffi aarch64 3.4.2-8.el9 baseos 38 k libgcc aarch64 11.5.0-11.el9 baseos 79 k libgcrypt aarch64 1.10.0-11.el9 baseos 458 k libgomp aarch64 11.5.0-11.el9 baseos 256 k libgpg-error aarch64 1.42-5.el9 baseos 217 k libidn2 aarch64 2.3.0-7.el9 baseos 105 k libmount aarch64 2.37.4-21.el9 baseos 134 k libnghttp2 aarch64 1.43.0-6.el9 baseos 74 k libpkgconf aarch64 1.7.3-10.el9 baseos 37 k libpsl aarch64 0.21.1-5.el9 baseos 66 k libpwquality aarch64 1.4.4-8.el9 baseos 123 k libselinux aarch64 3.6-3.el9 baseos 87 k libsemanage aarch64 3.6-5.el9_6 baseos 118 k libsepol aarch64 3.6-3.el9 baseos 319 k libsigsegv aarch64 2.13-4.el9 baseos 30 k libsmartcols aarch64 2.37.4-21.el9 baseos 64 k libssh aarch64 0.10.4-17.el9_7 baseos 210 k libssh-config noarch 0.10.4-17.el9_7 baseos 8.1 k libstdc++ aarch64 11.5.0-11.el9 baseos 705 k libtasn1 aarch64 4.16.0-9.el9 baseos 76 k libtool-ltdl aarch64 2.4.6-46.el9 baseos 37 k libunistring aarch64 0.9.10-15.el9 baseos 491 k libutempter aarch64 1.2.1-6.el9 baseos 30 k libuuid aarch64 2.37.4-21.el9 baseos 29 k libverto aarch64 0.3.2-3.el9 baseos 24 k libxcrypt aarch64 4.4.18-3.el9 baseos 125 k libxml2 aarch64 2.9.13-14.el9_7 baseos 730 k libzstd aarch64 1.5.5-1.el9 baseos 277 k lua-libs aarch64 5.4.4-4.el9 baseos 129 k lua-srpm-macros noarch 1-6.el9 appstream 10 k lz4-libs aarch64 1.9.3-5.el9 baseos 69 k mpfr aarch64 4.1.0-7.el9 baseos 242 k ncurses aarch64 6.2-12.20210508.el9 baseos 404 k ncurses-base noarch 6.2-12.20210508.el9 baseos 96 k ncurses-libs aarch64 6.2-12.20210508.el9 baseos 317 k ocaml-srpm-macros noarch 6-6.el9 appstream 9.1 k openblas-srpm-macros noarch 2-11.el9 appstream 8.6 k openldap aarch64 2.6.8-4.el9 baseos 285 k openssl aarch64 1:3.5.1-5.el9_7 baseos 1.5 M openssl-fips-provider aarch64 3.0.7-8.el9 baseos 9.1 k openssl-fips-provider-so aarch64 3.0.7-8.el9 baseos 513 k openssl-libs aarch64 1:3.5.1-5.el9_7 baseos 2.2 M p11-kit aarch64 0.25.3-3.el9_5 baseos 511 k p11-kit-trust aarch64 0.25.3-3.el9_5 baseos 142 k pam aarch64 1.5.1-26.el9_6 baseos 621 k pcre aarch64 8.44-4.el9 baseos 183 k pcre2 aarch64 10.40-6.el9 baseos 220 k pcre2-syntax noarch 10.40-6.el9 baseos 144 k perl-AutoLoader noarch 5.74-481.1.el9_6 appstream 21 k perl-B aarch64 1.80-481.1.el9_6 appstream 180 k perl-Carp noarch 1.50-460.el9 appstream 31 k perl-Class-Struct noarch 0.66-481.1.el9_6 appstream 22 k perl-Data-Dumper aarch64 2.174-462.el9 appstream 57 k perl-Digest noarch 1.19-4.el9 appstream 29 k perl-Digest-MD5 aarch64 2.58-4.el9 appstream 40 k perl-Encode aarch64 4:3.08-462.el9 appstream 1.7 M perl-Errno aarch64 1.30-481.1.el9_6 appstream 14 k perl-Exporter noarch 5.74-461.el9 appstream 34 k perl-Fcntl aarch64 1.13-481.1.el9_6 appstream 20 k perl-File-Basename noarch 2.85-481.1.el9_6 appstream 17 k perl-File-Path noarch 2.18-4.el9 appstream 38 k perl-File-Temp noarch 1:0.231.100-4.el9 appstream 63 k perl-File-stat noarch 1.09-481.1.el9_6 appstream 17 k perl-FileHandle noarch 2.03-481.1.el9_6 appstream 15 k perl-Getopt-Long noarch 1:2.52-4.el9 appstream 64 k perl-Getopt-Std noarch 1.12-481.1.el9_6 appstream 15 k perl-HTTP-Tiny noarch 0.076-462.el9 appstream 57 k perl-IO aarch64 1.43-481.1.el9_6 appstream 88 k perl-IO-Socket-IP noarch 0.41-5.el9 appstream 45 k perl-IO-Socket-SSL noarch 2.073-2.el9 appstream 221 k perl-IPC-Open3 noarch 1.21-481.1.el9_6 appstream 22 k perl-MIME-Base64 aarch64 3.16-4.el9 appstream 34 k perl-Mozilla-CA noarch 20200520-6.el9 appstream 14 k perl-Net-SSLeay aarch64 1.94-3.el9 appstream 415 k perl-POSIX aarch64 1.94-481.1.el9_6 appstream 96 k perl-PathTools aarch64 3.78-461.el9 appstream 92 k perl-Pod-Escapes noarch 1:1.07-460.el9 appstream 22 k perl-Pod-Perldoc noarch 3.28.01-461.el9 appstream 92 k perl-Pod-Simple noarch 1:3.42-4.el9 appstream 229 k perl-Pod-Usage noarch 4:2.01-4.el9 appstream 43 k perl-Scalar-List-Utils aarch64 4:1.56-462.el9 appstream 74 k perl-SelectSaver noarch 1.02-481.1.el9_6 appstream 11 k perl-Socket aarch64 4:2.031-4.el9 appstream 58 k perl-Storable aarch64 1:3.21-460.el9 appstream 96 k perl-Symbol noarch 1.08-481.1.el9_6 appstream 14 k perl-Term-ANSIColor noarch 5.01-461.el9 appstream 51 k perl-Term-Cap noarch 1.17-460.el9 appstream 24 k perl-Text-ParseWords noarch 3.30-460.el9 appstream 18 k perl-Text-Tabs+Wrap noarch 2013.0523-460.el9 appstream 25 k perl-Time-Local noarch 2:1.300-7.el9 appstream 37 k perl-URI noarch 5.09-3.el9 appstream 125 k perl-base noarch 2.27-481.1.el9_6 appstream 16 k perl-constant noarch 1.33-461.el9 appstream 25 k perl-if noarch 0.60.800-481.1.el9_6 appstream 14 k perl-interpreter aarch64 4:5.32.1-481.1.el9_6 appstream 70 k perl-libnet noarch 3.13-4.el9 appstream 134 k perl-libs aarch64 4:5.32.1-481.1.el9_6 appstream 2.2 M perl-mro aarch64 1.23-481.1.el9_6 appstream 27 k perl-overload noarch 1.31-481.1.el9_6 appstream 45 k perl-overloading noarch 0.02-481.1.el9_6 appstream 12 k perl-parent noarch 1:0.238-460.el9 appstream 16 k perl-podlators noarch 1:4.14-460.el9 appstream 118 k perl-srpm-macros noarch 1-41.el9 appstream 9.4 k perl-subs noarch 1.03-481.1.el9_6 appstream 11 k perl-vars noarch 1.05-481.1.el9_6 appstream 13 k pkgconf aarch64 1.7.3-10.el9 baseos 44 k pkgconf-m4 noarch 1.7.3-10.el9 baseos 16 k pkgconf-pkg-config aarch64 1.7.3-10.el9 baseos 12 k popt aarch64 1.18-8.el9 baseos 68 k publicsuffix-list-dafsa noarch 20210518-3.el9 baseos 59 k pyproject-srpm-macros noarch 1.16.2-1.el9 appstream 14 k python-srpm-macros noarch 3.9-54.el9 appstream 18 k qt5-srpm-macros noarch 5.15.9-1.el9 appstream 9.1 k qt6-srpm-macros noarch 6.6.2-1.el9 epel 8.7 k readline aarch64 8.1-4.el9 baseos 214 k rpm aarch64 4.16.1.3-39.el9 baseos 531 k rpm-build-libs aarch64 4.16.1.3-39.el9 baseos 85 k rpm-libs aarch64 4.16.1.3-39.el9 baseos 300 k rpmautospec-rpm-macros noarch 0.8.1-11.el9 epel 11 k rust-srpm-macros noarch 17-4.el9 appstream 11 k rust-srpm-macros-epel noarch 26.3-1.el9 epel 10 k setup noarch 2.13.7-10.el9 baseos 150 k shadow-utils aarch64 2:4.9-15.el9 baseos 1.2 M sqlite-libs aarch64 3.34.1-9.el9_7 baseos 636 k systemd-libs aarch64 252-55.el9_7.7 baseos 644 k tzdata noarch 2025c-1.el9 baseos 904 k util-linux-core aarch64 2.37.4-21.el9 baseos 465 k xz-libs aarch64 5.2.5-8.el9_0 baseos 92 k zip aarch64 3.0-35.el9 baseos 263 k zlib aarch64 1.2.11-40.el9 baseos 92 k zstd aarch64 1.5.5-1.el9 baseos 360 k Transaction Summary ================================================================================ Install 210 Packages Total download size: 68 M Installed size: 248 M Downloading Packages: (1/210): cracklib-2.9.6-27.el9.aarch64.rpm 1.0 MB/s | 99 kB 00:00 (2/210): basesystem-11-13.el9.noarch.rpm 82 kB/s | 8.0 kB 00:00 (3/210): cpio-2.13-16.el9.aarch64.rpm 2.0 MB/s | 278 kB 00:00 (4/210): ed-1.14.2-12.el9.aarch64.rpm 1.0 MB/s | 77 kB 00:00 (5/210): diffutils-3.7-12.el9.aarch64.rpm 3.3 MB/s | 396 kB 00:00 (6/210): cracklib-dicts-2.9.6-27.el9.aarch64.rp 23 MB/s | 3.6 MB 00:00 (7/210): gawk-5.1.0-6.el9.aarch64.rpm 12 MB/s | 1.0 MB 00:00 (8/210): grep-3.6-5.el9.aarch64.rpm 2.7 MB/s | 270 kB 00:00 (9/210): groff-base-1.22.4-10.el9.aarch64.rpm 12 MB/s | 1.0 MB 00:00 (10/210): json-c-0.14-11.el9.aarch64.rpm 578 kB/s | 44 kB 00:00 (11/210): libattr-2.5.1-3.el9.aarch64.rpm 268 kB/s | 20 kB 00:00 (12/210): info-6.7-15.el9.aarch64.rpm 1.3 MB/s | 225 kB 00:00 (13/210): libcap-ng-0.8.2-7.el9.aarch64.rpm 382 kB/s | 35 kB 00:00 (14/210): libgpg-error-1.42-5.el9.aarch64.rpm 2.7 MB/s | 217 kB 00:00 (15/210): libidn2-2.3.0-7.el9.aarch64.rpm 1.4 MB/s | 105 kB 00:00 (16/210): libpsl-0.21.1-5.el9.aarch64.rpm 517 kB/s | 66 kB 00:00 (17/210): libpwquality-1.4.4-8.el9.aarch64.rpm 1.0 MB/s | 123 kB 00:00 (18/210): libsigsegv-2.13-4.el9.aarch64.rpm 245 kB/s | 30 kB 00:00 (19/210): libutempter-1.2.1-6.el9.aarch64.rpm 248 kB/s | 30 kB 00:00 (20/210): libunistring-0.9.10-15.el9.aarch64.rp 3.3 MB/s | 491 kB 00:00 (21/210): libverto-0.3.2-3.el9.aarch64.rpm 176 kB/s | 24 kB 00:00 (22/210): libxcrypt-4.4.18-3.el9.aarch64.rpm 1.3 MB/s | 125 kB 00:00 (23/210): lz4-libs-1.9.3-5.el9.aarch64.rpm 868 kB/s | 69 kB 00:00 (24/210): mpfr-4.1.0-7.el9.aarch64.rpm 2.6 MB/s | 242 kB 00:00 (25/210): popt-1.18-8.el9.aarch64.rpm 918 kB/s | 68 kB 00:00 (26/210): publicsuffix-list-dafsa-20210518-3.el 771 kB/s | 59 kB 00:00 (27/210): readline-8.1-4.el9.aarch64.rpm 2.1 MB/s | 214 kB 00:00 (28/210): sed-4.8-9.el9.aarch64.rpm 3.2 MB/s | 307 kB 00:00 (29/210): xz-5.2.5-8.el9_0.aarch64.rpm 2.4 MB/s | 230 kB 00:00 (30/210): xz-libs-5.2.5-8.el9_0.aarch64.rpm 1.1 MB/s | 92 kB 00:00 (31/210): gzip-1.12-1.el9.aarch64.rpm 1.9 MB/s | 166 kB 00:00 (32/210): keyutils-libs-1.6.3-1.el9.aarch64.rpm 409 kB/s | 34 kB 00:00 (33/210): libpkgconf-1.7.3-10.el9.aarch64.rpm 459 kB/s | 37 kB 00:00 (34/210): pkgconf-1.7.3-10.el9.aarch64.rpm 556 kB/s | 44 kB 00:00 (35/210): pkgconf-m4-1.7.3-10.el9.noarch.rpm 192 kB/s | 16 kB 00:00 (36/210): zip-3.0-35.el9.aarch64.rpm 2.7 MB/s | 263 kB 00:00 (37/210): gmp-6.2.0-13.el9.aarch64.rpm 2.7 MB/s | 269 kB 00:00 (38/210): pkgconf-pkg-config-1.7.3-10.el9.aarch 87 kB/s | 12 kB 00:00 (39/210): libffi-3.4.2-8.el9.aarch64.rpm 342 kB/s | 38 kB 00:00 (40/210): lua-libs-5.4.4-4.el9.aarch64.rpm 1.3 MB/s | 129 kB 00:00 (41/210): zlib-1.2.11-40.el9.aarch64.rpm 877 kB/s | 92 kB 00:00 (42/210): file-5.39-16.el9.aarch64.rpm 579 kB/s | 52 kB 00:00 (43/210): bash-5.1.8-9.el9.aarch64.rpm 16 MB/s | 1.7 MB 00:00 (44/210): libacl-2.3.1-4.el9.aarch64.rpm 283 kB/s | 24 kB 00:00 (45/210): setup-2.13.7-10.el9.noarch.rpm 1.8 MB/s | 150 kB 00:00 (46/210): file-libs-5.39-16.el9.aarch64.rpm 6.9 MB/s | 591 kB 00:00 (47/210): libevent-2.1.12-8.el9_4.aarch64.rpm 1.8 MB/s | 260 kB 00:00 (48/210): findutils-4.8.0-7.el9.aarch64.rpm 6.6 MB/s | 552 kB 00:00 (49/210): gdbm-libs-1.23-1.el9.aarch64.rpm 676 kB/s | 59 kB 00:00 (50/210): libeconf-0.4.1-4.el9.aarch64.rpm 304 kB/s | 29 kB 00:00 (51/210): 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debugedit-5.0-11.el9.aarch64.rpm 987 kB/s | 77 kB 00:00 (194/210): efi-srpm-macros-6-4.el9.noarch.rpm 257 kB/s | 21 kB 00:00 (195/210): perl-Net-SSLeay-1.94-3.el9.aarch64.r 5.0 MB/s | 415 kB 00:00 (196/210): dwz-0.16-1.el9.aarch64.rpm 1.6 MB/s | 134 kB 00:00 (197/210): kernel-srpm-macros-1.0-14.el9.noarch 179 kB/s | 14 kB 00:00 (198/210): gdb-minimal-16.3-2.el9.aarch64.rpm 37 MB/s | 4.2 MB 00:00 (199/210): redhat-rpm-config-210-1.el9.noarch.r 892 kB/s | 70 kB 00:00 (200/210): ansible-srpm-macros-1-16.el9.noarch. 819 kB/s | 21 kB 00:00 (201/210): epel-rpm-macros-9-17.el9.noarch.rpm 2.2 MB/s | 15 kB 00:00 (202/210): forge-srpm-macros-0.4.0-1.el9.noarch 3.0 MB/s | 19 kB 00:00 (203/210): fpc-srpm-macros-1.3-7.el9.noarch.rpm 1.2 MB/s | 7.5 kB 00:00 (204/210): ghc-srpm-macros-epel-1.9.1-1.el9.noa 1.2 MB/s | 7.5 kB 00:00 (205/210): go-srpm-macros-epel-3.8.0-1.el9.noar 4.1 MB/s | 26 kB 00:00 (206/210): rpm-build-4.16.1.3-39.el9.aarch64.rp 782 kB/s | 66 kB 00:00 (207/210): qt6-srpm-macros-6.6.2-1.el9.noarch.r 1.4 MB/s | 8.7 kB 00:00 (208/210): rpmautospec-rpm-macros-0.8.1-11.el9. 981 kB/s | 11 kB 00:00 (209/210): rust-srpm-macros-epel-26.3-1.el9.noa 1.6 MB/s | 10 kB 00:00 (210/210): go-srpm-macros-3.6.0-12.el9_7.noarch 310 kB/s | 27 kB 00:00 -------------------------------------------------------------------------------- Total 11 MB/s | 68 MB 00:06 Red Hat Enterprise Linux - BaseOS 3.5 MB/s | 3.6 kB 00:00 Importing GPG key 0xFD431D51: Userid : "Red Hat, Inc. (release key 2) " Fingerprint: 567E 347A D004 4ADE 55BA 8A5F 199E 2F91 FD43 1D51 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat9-release Key imported successfully Importing GPG key 0x5A6340B3: Userid : "Red Hat, Inc. (auxiliary key 3) " Fingerprint: 7E46 2425 8C40 6535 D56D 6F13 5054 E4A4 5A63 40B3 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat9-release Key imported successfully Extra Packages for Enterprise Linux 9 - aarch64 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x3228467C: Userid : "Fedora (epel9) " Fingerprint: FF8A D134 4597 106E CE81 3B91 8A38 72BF 3228 467C From : /usr/share/distribution-gpg-keys/epel/RPM-GPG-KEY-EPEL-9 Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.16-5.el9.aarch64 1/1 Preparing : 1/1 Installing : rust-srpm-macros-17-4.el9.noarch 1/210 Installing : redhat-release-9.7-0.7.el9.aarch64 2/210 Installing : setup-2.13.7-10.el9.noarch 3/210 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.13.7-10.el9.noarch 3/210 Installing : filesystem-3.16-5.el9.aarch64 4/210 Installing : basesystem-11-13.el9.noarch 5/210 Installing : rust-srpm-macros-epel-26.3-1.el9.noarch 6/210 Installing : qt6-srpm-macros-6.6.2-1.el9.noarch 7/210 Installing : ghc-srpm-macros-epel-1.9.1-1.el9.noarch 8/210 Installing : fpc-srpm-macros-1.3-7.el9.noarch 9/210 Installing : ansible-srpm-macros-1-16.el9.noarch 10/210 Installing : qt5-srpm-macros-5.15.9-1.el9.noarch 11/210 Installing : ocaml-srpm-macros-6-6.el9.noarch 12/210 Installing : openblas-srpm-macros-2-11.el9.noarch 13/210 Installing : ghc-srpm-macros-1.5.0-6.el9.noarch 14/210 Installing : perl-srpm-macros-1-41.el9.noarch 15/210 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libacl-2.3.1-4.el9.aarch64 44/210 Verifying : setup-2.13.7-10.el9.noarch 45/210 Verifying : file-libs-5.39-16.el9.aarch64 46/210 Verifying : libevent-2.1.12-8.el9_4.aarch64 47/210 Verifying : filesystem-3.16-5.el9.aarch64 48/210 Verifying : findutils-1:4.8.0-7.el9.aarch64 49/210 Verifying : gdbm-libs-1:1.23-1.el9.aarch64 50/210 Verifying : libeconf-0.4.1-4.el9.aarch64 51/210 Verifying : libgcrypt-1.10.0-11.el9.aarch64 52/210 Verifying : libnghttp2-1.43.0-6.el9.aarch64 53/210 Verifying : pcre-8.44-4.el9.aarch64 54/210 Verifying : pcre2-10.40-6.el9.aarch64 55/210 Verifying : pcre2-syntax-10.40-6.el9.noarch 56/210 Verifying : bzip2-1.0.8-10.el9_5.aarch64 57/210 Verifying : bzip2-libs-1.0.8-10.el9_5.aarch64 58/210 Verifying : libbrotli-1.0.9-7.el9_5.aarch64 59/210 Verifying : p11-kit-0.25.3-3.el9_5.aarch64 60/210 Verifying : p11-kit-trust-0.25.3-3.el9_5.aarch64 61/210 Verifying : alternatives-1.24-2.el9.aarch64 62/210 Verifying : coreutils-8.32-39.el9.aarch64 63/210 Verifying : coreutils-common-8.32-39.el9.aarch64 64/210 Verifying : libblkid-2.37.4-21.el9.aarch64 65/210 Verifying : libfdisk-2.37.4-21.el9.aarch64 66/210 Verifying : libmount-2.37.4-21.el9.aarch64 67/210 Verifying : libselinux-3.6-3.el9.aarch64 68/210 Verifying : libsemanage-3.6-5.el9_6.aarch64 69/210 Verifying : libsmartcols-2.37.4-21.el9.aarch64 70/210 Verifying : libtasn1-4.16.0-9.el9.aarch64 71/210 Verifying : libtool-ltdl-2.4.6-46.el9.aarch64 72/210 Verifying : libuuid-2.37.4-21.el9.aarch64 73/210 Verifying : libzstd-1.5.5-1.el9.aarch64 74/210 Verifying : openldap-2.6.8-4.el9.aarch64 75/210 Verifying : util-linux-2.37.4-21.el9.aarch64 76/210 Verifying : util-linux-core-2.37.4-21.el9.aarch64 77/210 Verifying : zstd-1.5.5-1.el9.aarch64 78/210 Verifying : krb5-libs-1.21.1-8.el9_6.aarch64 79/210 Verifying : libarchive-3.5.3-6.el9_6.aarch64 80/210 Verifying : libdb-5.3.28-57.el9_6.aarch64 81/210 Verifying : which-2.21-30.el9_6.aarch64 82/210 Verifying : crypto-policies-20250905-1.git377cc42.el9_7.noar 83/210 Verifying : curl-7.76.1-34.el9.aarch64 84/210 Verifying : cyrus-sasl-lib-2.1.27-22.el9.aarch64 85/210 Verifying : elfutils-0.193-1.el9.aarch64 86/210 Verifying : elfutils-debuginfod-client-0.193-1.el9.aarch64 87/210 Verifying : elfutils-default-yama-scope-0.193-1.el9.noarch 88/210 Verifying : elfutils-libelf-0.193-1.el9.aarch64 89/210 Verifying : elfutils-libs-0.193-1.el9.aarch64 90/210 Verifying : libcap-2.48-10.el9.aarch64 91/210 Verifying : libcom_err-1.46.5-8.el9.aarch64 92/210 Verifying : libcurl-7.76.1-34.el9.aarch64 93/210 Verifying : libgcc-11.5.0-11.el9.aarch64 94/210 Verifying : libgomp-11.5.0-11.el9.aarch64 95/210 Verifying : libsepol-3.6-3.el9.aarch64 96/210 Verifying : libstdc++-11.5.0-11.el9.aarch64 97/210 Verifying : ncurses-base-6.2-12.20210508.el9.noarch 98/210 Verifying : ncurses-libs-6.2-12.20210508.el9.aarch64 99/210 Verifying : openssl-fips-provider-3.0.7-8.el9.aarch64 100/210 Verifying : openssl-fips-provider-so-3.0.7-8.el9.aarch64 101/210 Verifying : pam-1.5.1-26.el9_6.aarch64 102/210 Verifying : rpm-build-libs-4.16.1.3-39.el9.aarch64 103/210 Verifying : rpm-libs-4.16.1.3-39.el9.aarch64 104/210 Verifying : shadow-utils-2:4.9-15.el9.aarch64 105/210 Verifying : unzip-6.0-59.el9.aarch64 106/210 Verifying : audit-libs-3.1.5-7.el9.aarch64 107/210 Verifying : ncurses-6.2-12.20210508.el9.aarch64 108/210 Verifying : rpm-4.16.1.3-39.el9.aarch64 109/210 Verifying : glibc-2.34-231.el9_7.2.aarch64 110/210 Verifying : glibc-common-2.34-231.el9_7.2.aarch64 111/210 Verifying : glibc-gconv-extra-2.34-231.el9_7.2.aarch64 112/210 Verifying : glibc-minimal-langpack-2.34-231.el9_7.2.aarch64 113/210 Verifying : redhat-release-9.7-0.7.el9.aarch64 114/210 Verifying : sqlite-libs-3.34.1-9.el9_7.aarch64 115/210 Verifying : ca-certificates-2025.2.80_v9.0.305-91.el9.noarch 116/210 Verifying : libxml2-2.9.13-14.el9_7.aarch64 117/210 Verifying : systemd-libs-252-55.el9_7.7.aarch64 118/210 Verifying : tzdata-2025c-1.el9.noarch 119/210 Verifying : libssh-0.10.4-17.el9_7.aarch64 120/210 Verifying : libssh-config-0.10.4-17.el9_7.noarch 121/210 Verifying : binutils-2.35.2-67.el9_7.1.aarch64 122/210 Verifying : binutils-gold-2.35.2-67.el9_7.1.aarch64 123/210 Verifying : tar-2:1.34-9.el9_7.aarch64 124/210 Verifying : openssl-1:3.5.1-5.el9_7.aarch64 125/210 Verifying : openssl-libs-1:3.5.1-5.el9_7.aarch64 126/210 Verifying : perl-Exporter-5.74-461.el9.noarch 127/210 Verifying : perl-File-Temp-1:0.231.100-4.el9.noarch 128/210 Verifying : perl-IO-Socket-IP-0.41-5.el9.noarch 129/210 Verifying : perl-Mozilla-CA-20200520-6.el9.noarch 130/210 Verifying : perl-Term-Cap-1.17-460.el9.noarch 131/210 Verifying : perl-Time-Local-2:1.300-7.el9.noarch 132/210 Verifying : perl-parent-1:0.238-460.el9.noarch 133/210 Verifying : perl-srpm-macros-1-41.el9.noarch 134/210 Verifying : rust-srpm-macros-17-4.el9.noarch 135/210 Verifying : ghc-srpm-macros-1.5.0-6.el9.noarch 136/210 Verifying : openblas-srpm-macros-2-11.el9.noarch 137/210 Verifying : patch-2.7.6-16.el9.aarch64 138/210 Verifying : perl-Digest-MD5-2.58-4.el9.aarch64 139/210 Verifying : perl-MIME-Base64-3.16-4.el9.aarch64 140/210 Verifying : perl-Pod-Simple-1:3.42-4.el9.noarch 141/210 Verifying : perl-Pod-Usage-4:2.01-4.el9.noarch 142/210 Verifying : perl-Term-ANSIColor-5.01-461.el9.noarch 143/210 Verifying : perl-Text-ParseWords-3.30-460.el9.noarch 144/210 Verifying : perl-URI-5.09-3.el9.noarch 145/210 Verifying : perl-constant-1.33-461.el9.noarch 146/210 Verifying : perl-File-Path-2.18-4.el9.noarch 147/210 Verifying : perl-PathTools-3.78-461.el9.aarch64 148/210 Verifying : perl-Pod-Escapes-1:1.07-460.el9.noarch 149/210 Verifying : perl-Pod-Perldoc-3.28.01-461.el9.noarch 150/210 Verifying : perl-libnet-3.13-4.el9.noarch 151/210 Verifying : perl-podlators-1:4.14-460.el9.noarch 152/210 Verifying : fonts-srpm-macros-1:2.0.5-7.el9.1.noarch 153/210 Verifying : lua-srpm-macros-1-6.el9.noarch 154/210 Verifying : ocaml-srpm-macros-6-6.el9.noarch 155/210 Verifying : perl-Carp-1.50-460.el9.noarch 156/210 Verifying : perl-Data-Dumper-2.174-462.el9.aarch64 157/210 Verifying : perl-Digest-1.19-4.el9.noarch 158/210 Verifying : perl-Encode-4:3.08-462.el9.aarch64 159/210 Verifying : perl-Getopt-Long-1:2.52-4.el9.noarch 160/210 Verifying : perl-Socket-4:2.031-4.el9.aarch64 161/210 Verifying : perl-Storable-1:3.21-460.el9.aarch64 162/210 Verifying : perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch 163/210 Verifying : qt5-srpm-macros-5.15.9-1.el9.noarch 164/210 Verifying : perl-HTTP-Tiny-0.076-462.el9.noarch 165/210 Verifying : perl-Scalar-List-Utils-4:1.56-462.el9.aarch64 166/210 Verifying : python-srpm-macros-3.9-54.el9.noarch 167/210 Verifying : perl-IO-Socket-SSL-2.073-2.el9.noarch 168/210 Verifying : pyproject-srpm-macros-1.16.2-1.el9.noarch 169/210 Verifying : perl-AutoLoader-5.74-481.1.el9_6.noarch 170/210 Verifying : perl-B-1.80-481.1.el9_6.aarch64 171/210 Verifying : perl-Class-Struct-0.66-481.1.el9_6.noarch 172/210 Verifying : perl-Errno-1.30-481.1.el9_6.aarch64 173/210 Verifying : perl-Fcntl-1.13-481.1.el9_6.aarch64 174/210 Verifying : perl-File-Basename-2.85-481.1.el9_6.noarch 175/210 Verifying : perl-File-stat-1.09-481.1.el9_6.noarch 176/210 Verifying : perl-FileHandle-2.03-481.1.el9_6.noarch 177/210 Verifying : perl-Getopt-Std-1.12-481.1.el9_6.noarch 178/210 Verifying : perl-IO-1.43-481.1.el9_6.aarch64 179/210 Verifying : perl-IPC-Open3-1.21-481.1.el9_6.noarch 180/210 Verifying : perl-POSIX-1.94-481.1.el9_6.aarch64 181/210 Verifying : perl-SelectSaver-1.02-481.1.el9_6.noarch 182/210 Verifying : perl-Symbol-1.08-481.1.el9_6.noarch 183/210 Verifying : perl-base-2.27-481.1.el9_6.noarch 184/210 Verifying : perl-if-0.60.800-481.1.el9_6.noarch 185/210 Verifying : perl-interpreter-4:5.32.1-481.1.el9_6.aarch64 186/210 Verifying : perl-libs-4:5.32.1-481.1.el9_6.aarch64 187/210 Verifying : perl-mro-1.23-481.1.el9_6.aarch64 188/210 Verifying : perl-overload-1.31-481.1.el9_6.noarch 189/210 Verifying : perl-overloading-0.02-481.1.el9_6.noarch 190/210 Verifying : perl-subs-1.03-481.1.el9_6.noarch 191/210 Verifying : perl-vars-1.05-481.1.el9_6.noarch 192/210 Verifying : debugedit-5.0-11.el9.aarch64 193/210 Verifying : efi-srpm-macros-6-4.el9.noarch 194/210 Verifying : perl-Net-SSLeay-1.94-3.el9.aarch64 195/210 Verifying : dwz-0.16-1.el9.aarch64 196/210 Verifying : gdb-minimal-16.3-2.el9.aarch64 197/210 Verifying : kernel-srpm-macros-1.0-14.el9.noarch 198/210 Verifying : redhat-rpm-config-210-1.el9.noarch 199/210 Verifying : rpm-build-4.16.1.3-39.el9.aarch64 200/210 Verifying : go-srpm-macros-3.6.0-12.el9_7.noarch 201/210 Verifying : ansible-srpm-macros-1-16.el9.noarch 202/210 Verifying : epel-rpm-macros-9-17.el9.noarch 203/210 Verifying : forge-srpm-macros-0.4.0-1.el9.noarch 204/210 Verifying : fpc-srpm-macros-1.3-7.el9.noarch 205/210 Verifying : ghc-srpm-macros-epel-1.9.1-1.el9.noarch 206/210 Verifying : go-srpm-macros-epel-3.8.0-1.el9.noarch 207/210 Verifying : qt6-srpm-macros-6.6.2-1.el9.noarch 208/210 Verifying : rpmautospec-rpm-macros-0.8.1-11.el9.noarch 209/210 Verifying : rust-srpm-macros-epel-26.3-1.el9.noarch 210/210 Installed products updated. Installed: alternatives-1.24-2.el9.aarch64 ansible-srpm-macros-1-16.el9.noarch audit-libs-3.1.5-7.el9.aarch64 basesystem-11-13.el9.noarch bash-5.1.8-9.el9.aarch64 binutils-2.35.2-67.el9_7.1.aarch64 binutils-gold-2.35.2-67.el9_7.1.aarch64 bzip2-1.0.8-10.el9_5.aarch64 bzip2-libs-1.0.8-10.el9_5.aarch64 ca-certificates-2025.2.80_v9.0.305-91.el9.noarch coreutils-8.32-39.el9.aarch64 coreutils-common-8.32-39.el9.aarch64 cpio-2.13-16.el9.aarch64 cracklib-2.9.6-27.el9.aarch64 cracklib-dicts-2.9.6-27.el9.aarch64 crypto-policies-20250905-1.git377cc42.el9_7.noarch curl-7.76.1-34.el9.aarch64 cyrus-sasl-lib-2.1.27-22.el9.aarch64 debugedit-5.0-11.el9.aarch64 diffutils-3.7-12.el9.aarch64 dwz-0.16-1.el9.aarch64 ed-1.14.2-12.el9.aarch64 efi-srpm-macros-6-4.el9.noarch elfutils-0.193-1.el9.aarch64 elfutils-debuginfod-client-0.193-1.el9.aarch64 elfutils-default-yama-scope-0.193-1.el9.noarch elfutils-libelf-0.193-1.el9.aarch64 elfutils-libs-0.193-1.el9.aarch64 epel-rpm-macros-9-17.el9.noarch file-5.39-16.el9.aarch64 file-libs-5.39-16.el9.aarch64 filesystem-3.16-5.el9.aarch64 findutils-1:4.8.0-7.el9.aarch64 fonts-srpm-macros-1:2.0.5-7.el9.1.noarch forge-srpm-macros-0.4.0-1.el9.noarch fpc-srpm-macros-1.3-7.el9.noarch gawk-5.1.0-6.el9.aarch64 gdb-minimal-16.3-2.el9.aarch64 gdbm-libs-1:1.23-1.el9.aarch64 ghc-srpm-macros-1.5.0-6.el9.noarch ghc-srpm-macros-epel-1.9.1-1.el9.noarch glibc-2.34-231.el9_7.2.aarch64 glibc-common-2.34-231.el9_7.2.aarch64 glibc-gconv-extra-2.34-231.el9_7.2.aarch64 glibc-minimal-langpack-2.34-231.el9_7.2.aarch64 gmp-1:6.2.0-13.el9.aarch64 go-srpm-macros-3.6.0-12.el9_7.noarch go-srpm-macros-epel-3.8.0-1.el9.noarch grep-3.6-5.el9.aarch64 groff-base-1.22.4-10.el9.aarch64 gzip-1.12-1.el9.aarch64 info-6.7-15.el9.aarch64 json-c-0.14-11.el9.aarch64 kernel-srpm-macros-1.0-14.el9.noarch keyutils-libs-1.6.3-1.el9.aarch64 krb5-libs-1.21.1-8.el9_6.aarch64 libacl-2.3.1-4.el9.aarch64 libarchive-3.5.3-6.el9_6.aarch64 libattr-2.5.1-3.el9.aarch64 libblkid-2.37.4-21.el9.aarch64 libbrotli-1.0.9-7.el9_5.aarch64 libcap-2.48-10.el9.aarch64 libcap-ng-0.8.2-7.el9.aarch64 libcom_err-1.46.5-8.el9.aarch64 libcurl-7.76.1-34.el9.aarch64 libdb-5.3.28-57.el9_6.aarch64 libeconf-0.4.1-4.el9.aarch64 libevent-2.1.12-8.el9_4.aarch64 libfdisk-2.37.4-21.el9.aarch64 libffi-3.4.2-8.el9.aarch64 libgcc-11.5.0-11.el9.aarch64 libgcrypt-1.10.0-11.el9.aarch64 libgomp-11.5.0-11.el9.aarch64 libgpg-error-1.42-5.el9.aarch64 libidn2-2.3.0-7.el9.aarch64 libmount-2.37.4-21.el9.aarch64 libnghttp2-1.43.0-6.el9.aarch64 libpkgconf-1.7.3-10.el9.aarch64 libpsl-0.21.1-5.el9.aarch64 libpwquality-1.4.4-8.el9.aarch64 libselinux-3.6-3.el9.aarch64 libsemanage-3.6-5.el9_6.aarch64 libsepol-3.6-3.el9.aarch64 libsigsegv-2.13-4.el9.aarch64 libsmartcols-2.37.4-21.el9.aarch64 libssh-0.10.4-17.el9_7.aarch64 libssh-config-0.10.4-17.el9_7.noarch libstdc++-11.5.0-11.el9.aarch64 libtasn1-4.16.0-9.el9.aarch64 libtool-ltdl-2.4.6-46.el9.aarch64 libunistring-0.9.10-15.el9.aarch64 libutempter-1.2.1-6.el9.aarch64 libuuid-2.37.4-21.el9.aarch64 libverto-0.3.2-3.el9.aarch64 libxcrypt-4.4.18-3.el9.aarch64 libxml2-2.9.13-14.el9_7.aarch64 libzstd-1.5.5-1.el9.aarch64 lua-libs-5.4.4-4.el9.aarch64 lua-srpm-macros-1-6.el9.noarch lz4-libs-1.9.3-5.el9.aarch64 mpfr-4.1.0-7.el9.aarch64 ncurses-6.2-12.20210508.el9.aarch64 ncurses-base-6.2-12.20210508.el9.noarch ncurses-libs-6.2-12.20210508.el9.aarch64 ocaml-srpm-macros-6-6.el9.noarch openblas-srpm-macros-2-11.el9.noarch openldap-2.6.8-4.el9.aarch64 openssl-1:3.5.1-5.el9_7.aarch64 openssl-fips-provider-3.0.7-8.el9.aarch64 openssl-fips-provider-so-3.0.7-8.el9.aarch64 openssl-libs-1:3.5.1-5.el9_7.aarch64 p11-kit-0.25.3-3.el9_5.aarch64 p11-kit-trust-0.25.3-3.el9_5.aarch64 pam-1.5.1-26.el9_6.aarch64 patch-2.7.6-16.el9.aarch64 pcre-8.44-4.el9.aarch64 pcre2-10.40-6.el9.aarch64 pcre2-syntax-10.40-6.el9.noarch perl-AutoLoader-5.74-481.1.el9_6.noarch perl-B-1.80-481.1.el9_6.aarch64 perl-Carp-1.50-460.el9.noarch perl-Class-Struct-0.66-481.1.el9_6.noarch perl-Data-Dumper-2.174-462.el9.aarch64 perl-Digest-1.19-4.el9.noarch perl-Digest-MD5-2.58-4.el9.aarch64 perl-Encode-4:3.08-462.el9.aarch64 perl-Errno-1.30-481.1.el9_6.aarch64 perl-Exporter-5.74-461.el9.noarch perl-Fcntl-1.13-481.1.el9_6.aarch64 perl-File-Basename-2.85-481.1.el9_6.noarch perl-File-Path-2.18-4.el9.noarch perl-File-Temp-1:0.231.100-4.el9.noarch perl-File-stat-1.09-481.1.el9_6.noarch perl-FileHandle-2.03-481.1.el9_6.noarch perl-Getopt-Long-1:2.52-4.el9.noarch perl-Getopt-Std-1.12-481.1.el9_6.noarch perl-HTTP-Tiny-0.076-462.el9.noarch perl-IO-1.43-481.1.el9_6.aarch64 perl-IO-Socket-IP-0.41-5.el9.noarch perl-IO-Socket-SSL-2.073-2.el9.noarch perl-IPC-Open3-1.21-481.1.el9_6.noarch perl-MIME-Base64-3.16-4.el9.aarch64 perl-Mozilla-CA-20200520-6.el9.noarch perl-Net-SSLeay-1.94-3.el9.aarch64 perl-POSIX-1.94-481.1.el9_6.aarch64 perl-PathTools-3.78-461.el9.aarch64 perl-Pod-Escapes-1:1.07-460.el9.noarch perl-Pod-Perldoc-3.28.01-461.el9.noarch perl-Pod-Simple-1:3.42-4.el9.noarch perl-Pod-Usage-4:2.01-4.el9.noarch perl-Scalar-List-Utils-4:1.56-462.el9.aarch64 perl-SelectSaver-1.02-481.1.el9_6.noarch perl-Socket-4:2.031-4.el9.aarch64 perl-Storable-1:3.21-460.el9.aarch64 perl-Symbol-1.08-481.1.el9_6.noarch perl-Term-ANSIColor-5.01-461.el9.noarch perl-Term-Cap-1.17-460.el9.noarch perl-Text-ParseWords-3.30-460.el9.noarch perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch perl-Time-Local-2:1.300-7.el9.noarch perl-URI-5.09-3.el9.noarch perl-base-2.27-481.1.el9_6.noarch perl-constant-1.33-461.el9.noarch perl-if-0.60.800-481.1.el9_6.noarch perl-interpreter-4:5.32.1-481.1.el9_6.aarch64 perl-libnet-3.13-4.el9.noarch perl-libs-4:5.32.1-481.1.el9_6.aarch64 perl-mro-1.23-481.1.el9_6.aarch64 perl-overload-1.31-481.1.el9_6.noarch perl-overloading-0.02-481.1.el9_6.noarch perl-parent-1:0.238-460.el9.noarch perl-podlators-1:4.14-460.el9.noarch perl-srpm-macros-1-41.el9.noarch perl-subs-1.03-481.1.el9_6.noarch perl-vars-1.05-481.1.el9_6.noarch pkgconf-1.7.3-10.el9.aarch64 pkgconf-m4-1.7.3-10.el9.noarch pkgconf-pkg-config-1.7.3-10.el9.aarch64 popt-1.18-8.el9.aarch64 publicsuffix-list-dafsa-20210518-3.el9.noarch pyproject-srpm-macros-1.16.2-1.el9.noarch python-srpm-macros-3.9-54.el9.noarch qt5-srpm-macros-5.15.9-1.el9.noarch qt6-srpm-macros-6.6.2-1.el9.noarch readline-8.1-4.el9.aarch64 redhat-release-9.7-0.7.el9.aarch64 redhat-rpm-config-210-1.el9.noarch rpm-4.16.1.3-39.el9.aarch64 rpm-build-4.16.1.3-39.el9.aarch64 rpm-build-libs-4.16.1.3-39.el9.aarch64 rpm-libs-4.16.1.3-39.el9.aarch64 rpmautospec-rpm-macros-0.8.1-11.el9.noarch rust-srpm-macros-17-4.el9.noarch rust-srpm-macros-epel-26.3-1.el9.noarch sed-4.8-9.el9.aarch64 setup-2.13.7-10.el9.noarch shadow-utils-2:4.9-15.el9.aarch64 sqlite-libs-3.34.1-9.el9_7.aarch64 systemd-libs-252-55.el9_7.7.aarch64 tar-2:1.34-9.el9_7.aarch64 tzdata-2025c-1.el9.noarch unzip-6.0-59.el9.aarch64 util-linux-2.37.4-21.el9.aarch64 util-linux-core-2.37.4-21.el9.aarch64 which-2.21-30.el9_6.aarch64 xz-5.2.5-8.el9_0.aarch64 xz-libs-5.2.5-8.el9_0.aarch64 zip-3.0-35.el9.aarch64 zlib-1.2.11-40.el9.aarch64 zstd-1.5.5-1.el9.aarch64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.24-2.el9.aarch64 ansible-srpm-macros-1-16.el9.noarch audit-libs-3.1.5-7.el9.aarch64 basesystem-11-13.el9.noarch bash-5.1.8-9.el9.aarch64 binutils-2.35.2-67.el9_7.1.aarch64 binutils-gold-2.35.2-67.el9_7.1.aarch64 bzip2-1.0.8-10.el9_5.aarch64 bzip2-libs-1.0.8-10.el9_5.aarch64 ca-certificates-2025.2.80_v9.0.305-91.el9.noarch coreutils-8.32-39.el9.aarch64 coreutils-common-8.32-39.el9.aarch64 cpio-2.13-16.el9.aarch64 cracklib-2.9.6-27.el9.aarch64 cracklib-dicts-2.9.6-27.el9.aarch64 crypto-policies-20250905-1.git377cc42.el9_7.noarch curl-7.76.1-34.el9.aarch64 cyrus-sasl-lib-2.1.27-22.el9.aarch64 debugedit-5.0-11.el9.aarch64 diffutils-3.7-12.el9.aarch64 dwz-0.16-1.el9.aarch64 ed-1.14.2-12.el9.aarch64 efi-srpm-macros-6-4.el9.noarch elfutils-0.193-1.el9.aarch64 elfutils-debuginfod-client-0.193-1.el9.aarch64 elfutils-default-yama-scope-0.193-1.el9.noarch elfutils-libelf-0.193-1.el9.aarch64 elfutils-libs-0.193-1.el9.aarch64 epel-rpm-macros-9-17.el9.noarch file-5.39-16.el9.aarch64 file-libs-5.39-16.el9.aarch64 filesystem-3.16-5.el9.aarch64 findutils-4.8.0-7.el9.aarch64 fonts-srpm-macros-2.0.5-7.el9.1.noarch forge-srpm-macros-0.4.0-1.el9.noarch fpc-srpm-macros-1.3-7.el9.noarch gawk-5.1.0-6.el9.aarch64 gdb-minimal-16.3-2.el9.aarch64 gdbm-libs-1.23-1.el9.aarch64 ghc-srpm-macros-1.5.0-6.el9.noarch ghc-srpm-macros-epel-1.9.1-1.el9.noarch glibc-2.34-231.el9_7.2.aarch64 glibc-common-2.34-231.el9_7.2.aarch64 glibc-gconv-extra-2.34-231.el9_7.2.aarch64 glibc-minimal-langpack-2.34-231.el9_7.2.aarch64 gmp-6.2.0-13.el9.aarch64 go-srpm-macros-3.6.0-12.el9_7.noarch go-srpm-macros-epel-3.8.0-1.el9.noarch gpg-pubkey-3228467c-613798eb gpg-pubkey-5a6340b3-6229229e gpg-pubkey-fd431d51-4ae0493b grep-3.6-5.el9.aarch64 groff-base-1.22.4-10.el9.aarch64 gzip-1.12-1.el9.aarch64 info-6.7-15.el9.aarch64 json-c-0.14-11.el9.aarch64 kernel-srpm-macros-1.0-14.el9.noarch keyutils-libs-1.6.3-1.el9.aarch64 krb5-libs-1.21.1-8.el9_6.aarch64 libacl-2.3.1-4.el9.aarch64 libarchive-3.5.3-6.el9_6.aarch64 libattr-2.5.1-3.el9.aarch64 libblkid-2.37.4-21.el9.aarch64 libbrotli-1.0.9-7.el9_5.aarch64 libcap-2.48-10.el9.aarch64 libcap-ng-0.8.2-7.el9.aarch64 libcom_err-1.46.5-8.el9.aarch64 libcurl-7.76.1-34.el9.aarch64 libdb-5.3.28-57.el9_6.aarch64 libeconf-0.4.1-4.el9.aarch64 libevent-2.1.12-8.el9_4.aarch64 libfdisk-2.37.4-21.el9.aarch64 libffi-3.4.2-8.el9.aarch64 libgcc-11.5.0-11.el9.aarch64 libgcrypt-1.10.0-11.el9.aarch64 libgomp-11.5.0-11.el9.aarch64 libgpg-error-1.42-5.el9.aarch64 libidn2-2.3.0-7.el9.aarch64 libmount-2.37.4-21.el9.aarch64 libnghttp2-1.43.0-6.el9.aarch64 libpkgconf-1.7.3-10.el9.aarch64 libpsl-0.21.1-5.el9.aarch64 libpwquality-1.4.4-8.el9.aarch64 libselinux-3.6-3.el9.aarch64 libsemanage-3.6-5.el9_6.aarch64 libsepol-3.6-3.el9.aarch64 libsigsegv-2.13-4.el9.aarch64 libsmartcols-2.37.4-21.el9.aarch64 libssh-0.10.4-17.el9_7.aarch64 libssh-config-0.10.4-17.el9_7.noarch libstdc++-11.5.0-11.el9.aarch64 libtasn1-4.16.0-9.el9.aarch64 libtool-ltdl-2.4.6-46.el9.aarch64 libunistring-0.9.10-15.el9.aarch64 libutempter-1.2.1-6.el9.aarch64 libuuid-2.37.4-21.el9.aarch64 libverto-0.3.2-3.el9.aarch64 libxcrypt-4.4.18-3.el9.aarch64 libxml2-2.9.13-14.el9_7.aarch64 libzstd-1.5.5-1.el9.aarch64 lua-libs-5.4.4-4.el9.aarch64 lua-srpm-macros-1-6.el9.noarch lz4-libs-1.9.3-5.el9.aarch64 mpfr-4.1.0-7.el9.aarch64 ncurses-6.2-12.20210508.el9.aarch64 ncurses-base-6.2-12.20210508.el9.noarch ncurses-libs-6.2-12.20210508.el9.aarch64 ocaml-srpm-macros-6-6.el9.noarch openblas-srpm-macros-2-11.el9.noarch openldap-2.6.8-4.el9.aarch64 openssl-3.5.1-5.el9_7.aarch64 openssl-fips-provider-3.0.7-8.el9.aarch64 openssl-fips-provider-so-3.0.7-8.el9.aarch64 openssl-libs-3.5.1-5.el9_7.aarch64 p11-kit-0.25.3-3.el9_5.aarch64 p11-kit-trust-0.25.3-3.el9_5.aarch64 pam-1.5.1-26.el9_6.aarch64 patch-2.7.6-16.el9.aarch64 pcre-8.44-4.el9.aarch64 pcre2-10.40-6.el9.aarch64 pcre2-syntax-10.40-6.el9.noarch perl-AutoLoader-5.74-481.1.el9_6.noarch perl-B-1.80-481.1.el9_6.aarch64 perl-Carp-1.50-460.el9.noarch perl-Class-Struct-0.66-481.1.el9_6.noarch perl-Data-Dumper-2.174-462.el9.aarch64 perl-Digest-1.19-4.el9.noarch perl-Digest-MD5-2.58-4.el9.aarch64 perl-Encode-3.08-462.el9.aarch64 perl-Errno-1.30-481.1.el9_6.aarch64 perl-Exporter-5.74-461.el9.noarch perl-Fcntl-1.13-481.1.el9_6.aarch64 perl-File-Basename-2.85-481.1.el9_6.noarch perl-File-Path-2.18-4.el9.noarch perl-File-Temp-0.231.100-4.el9.noarch perl-File-stat-1.09-481.1.el9_6.noarch perl-FileHandle-2.03-481.1.el9_6.noarch perl-Getopt-Long-2.52-4.el9.noarch perl-Getopt-Std-1.12-481.1.el9_6.noarch perl-HTTP-Tiny-0.076-462.el9.noarch perl-IO-1.43-481.1.el9_6.aarch64 perl-IO-Socket-IP-0.41-5.el9.noarch perl-IO-Socket-SSL-2.073-2.el9.noarch perl-IPC-Open3-1.21-481.1.el9_6.noarch perl-MIME-Base64-3.16-4.el9.aarch64 perl-Mozilla-CA-20200520-6.el9.noarch perl-Net-SSLeay-1.94-3.el9.aarch64 perl-POSIX-1.94-481.1.el9_6.aarch64 perl-PathTools-3.78-461.el9.aarch64 perl-Pod-Escapes-1.07-460.el9.noarch perl-Pod-Perldoc-3.28.01-461.el9.noarch perl-Pod-Simple-3.42-4.el9.noarch perl-Pod-Usage-2.01-4.el9.noarch perl-Scalar-List-Utils-1.56-462.el9.aarch64 perl-SelectSaver-1.02-481.1.el9_6.noarch perl-Socket-2.031-4.el9.aarch64 perl-Storable-3.21-460.el9.aarch64 perl-Symbol-1.08-481.1.el9_6.noarch perl-Term-ANSIColor-5.01-461.el9.noarch perl-Term-Cap-1.17-460.el9.noarch perl-Text-ParseWords-3.30-460.el9.noarch perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch perl-Time-Local-1.300-7.el9.noarch perl-URI-5.09-3.el9.noarch perl-base-2.27-481.1.el9_6.noarch perl-constant-1.33-461.el9.noarch perl-if-0.60.800-481.1.el9_6.noarch perl-interpreter-5.32.1-481.1.el9_6.aarch64 perl-libnet-3.13-4.el9.noarch perl-libs-5.32.1-481.1.el9_6.aarch64 perl-mro-1.23-481.1.el9_6.aarch64 perl-overload-1.31-481.1.el9_6.noarch perl-overloading-0.02-481.1.el9_6.noarch perl-parent-0.238-460.el9.noarch perl-podlators-4.14-460.el9.noarch perl-srpm-macros-1-41.el9.noarch perl-subs-1.03-481.1.el9_6.noarch perl-vars-1.05-481.1.el9_6.noarch pkgconf-1.7.3-10.el9.aarch64 pkgconf-m4-1.7.3-10.el9.noarch pkgconf-pkg-config-1.7.3-10.el9.aarch64 popt-1.18-8.el9.aarch64 publicsuffix-list-dafsa-20210518-3.el9.noarch pyproject-srpm-macros-1.16.2-1.el9.noarch python-srpm-macros-3.9-54.el9.noarch qt5-srpm-macros-5.15.9-1.el9.noarch qt6-srpm-macros-6.6.2-1.el9.noarch readline-8.1-4.el9.aarch64 redhat-release-9.7-0.7.el9.aarch64 redhat-rpm-config-210-1.el9.noarch rpm-4.16.1.3-39.el9.aarch64 rpm-build-4.16.1.3-39.el9.aarch64 rpm-build-libs-4.16.1.3-39.el9.aarch64 rpm-libs-4.16.1.3-39.el9.aarch64 rpmautospec-rpm-macros-0.8.1-11.el9.noarch rust-srpm-macros-17-4.el9.noarch rust-srpm-macros-epel-26.3-1.el9.noarch sed-4.8-9.el9.aarch64 setup-2.13.7-10.el9.noarch shadow-utils-4.9-15.el9.aarch64 sqlite-libs-3.34.1-9.el9_7.aarch64 systemd-libs-252-55.el9_7.7.aarch64 tar-1.34-9.el9_7.aarch64 tzdata-2025c-1.el9.noarch unzip-6.0-59.el9.aarch64 util-linux-2.37.4-21.el9.aarch64 util-linux-core-2.37.4-21.el9.aarch64 which-2.21-30.el9_6.aarch64 xz-5.2.5-8.el9_0.aarch64 xz-libs-5.2.5-8.el9_0.aarch64 zip-3.0-35.el9.aarch64 zlib-1.2.11-40.el9.aarch64 zstd-1.5.5-1.el9.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769385600 Wrote: /builddir/build/SRPMS/bcftools-1.23-1.el9.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-9-aarch64-1769508937.072208/root/var/log/dnf.rpm.log /var/lib/mock/rhel+epel-9-aarch64-1769508937.072208/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-9-aarch64-1769508937.072208/root/var/log/dnf.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-b4_0l74n/bcftools/bcftools.spec) Config(child) 1 minutes 13 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-1.23-1.el9.src.rpm) Config(rhel+epel-9-aarch64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-aarch64-bootstrap-1769508937.072208/root. INFO: reusing tmpfs at /var/lib/mock/rhel+epel-9-aarch64-bootstrap-1769508937.072208/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/rhel+epel-9-aarch64-1769508937.072208/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-4.16.1.3-39.el9.aarch64 python3-dnf-4.14.0-31.el9.noarch python3-dnf-plugins-core-4.3.0-24.el9_7.noarch yum-4.14.0-31.el9.noarch Finish: chroot init Start: build phase for bcftools-1.23-1.el9.src.rpm Start: build setup for bcftools-1.23-1.el9.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769385600 Wrote: /builddir/build/SRPMS/bcftools-1.23-1.el9.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 50 kB/s | 1.5 kB 00:00 Copr repository 92 kB/s | 7.4 kB 00:00 Red Hat Enterprise Linux - BaseOS 34 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux - AppStream 39 kB/s | 4.5 kB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 46 kB/s | 4.5 kB 00:00 Extra Packages for Enterprise Linux 9 - aarch64 51 kB/s | 12 kB 00:00 Package perl-File-Temp-1:0.231.100-4.el9.noarch is already installed. Package perl-Getopt-Long-1:2.52-4.el9.noarch is already installed. Package perl-interpreter-4:5.32.1-481.1.el9_6.aarch64 is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: autoconf noarch 2.69-41.el9 appstream 681 k automake noarch 1.16.2-8.el9 appstream 693 k gcc aarch64 11.5.0-11.el9 appstream 30 M gsl-devel aarch64 2.6-7.el9 appstream 652 k htslib-devel aarch64 1.23-1.el9 copr_base 107 k htslib-tools aarch64 1.23-1.el9 copr_base 715 k make aarch64 1:4.3-8.el9 baseos 537 k perl-ExtUtils-Embed noarch 1.35-481.1.el9_6 appstream 17 k perl-FindBin noarch 1.51-481.1.el9_6 appstream 14 k zlib-devel aarch64 1.2.11-40.el9 appstream 47 k Installing dependencies: annobin aarch64 12.98-1.el9 appstream 1.1 M cpp aarch64 11.5.0-11.el9 appstream 10 M emacs-filesystem noarch 1:27.2-18.el9 appstream 9.3 k expat aarch64 2.5.0-5.el9_7.1 baseos 112 k gcc-plugin-annobin aarch64 11.5.0-11.el9 appstream 36 k glibc-devel aarch64 2.34-231.el9_7.2 appstream 555 k gsl aarch64 2.6-7.el9 appstream 1.0 M htslib aarch64 1.23-1.el9 copr_base 542 k kernel-headers aarch64 5.14.0-611.26.1.el9_7 appstream 2.8 M libasan aarch64 11.5.0-11.el9 appstream 399 k libatomic aarch64 11.5.0-11.el9 baseos 25 k libedit aarch64 3.1-38.20210216cvs.el9 baseos 105 k libmpc aarch64 1.2.1-4.el9 appstream 66 k libubsan aarch64 11.5.0-11.el9 appstream 175 k libxcrypt-devel aarch64 4.4.18-3.el9 appstream 32 k llvm-filesystem aarch64 20.1.8-3.el9 appstream 9.1 k llvm-libs aarch64 20.1.8-3.el9 appstream 28 M m4 aarch64 1.4.19-1.el9 appstream 301 k perl-AutoSplit noarch 5.74-481.1.el9_6 appstream 21 k perl-Benchmark noarch 1.23-481.1.el9_6 appstream 26 k perl-Devel-PPPort aarch64 3.62-4.el9 appstream 212 k perl-DynaLoader aarch64 1.47-481.1.el9_6 appstream 25 k perl-ExtUtils-Command noarch 2:7.60-3.el9 appstream 16 k perl-ExtUtils-Constant noarch 0.25-481.1.el9_6 appstream 46 k perl-ExtUtils-Install noarch 2.20-4.el9 appstream 47 k perl-ExtUtils-MakeMaker noarch 2:7.60-3.el9 appstream 304 k perl-ExtUtils-Manifest noarch 1:1.73-4.el9 appstream 37 k perl-ExtUtils-ParseXS noarch 1:3.40-460.el9 appstream 190 k perl-File-Compare noarch 1.100.600-481.1.el9_6 appstream 13 k perl-File-Copy noarch 2.34-481.1.el9_6 appstream 20 k perl-File-Find noarch 1.37-481.1.el9_6 appstream 25 k perl-Test-Harness noarch 1:3.42-461.el9 appstream 299 k perl-Thread-Queue noarch 3.14-460.el9 appstream 24 k perl-devel aarch64 4:5.32.1-481.1.el9_6 appstream 676 k perl-lib aarch64 0.65-481.1.el9_6 appstream 14 k perl-locale noarch 1.09-481.1.el9_6 appstream 13 k perl-threads aarch64 1:2.25-460.el9 appstream 60 k perl-threads-shared aarch64 1.61-460.el9 appstream 47 k perl-version aarch64 7:0.99.28-4.el9 appstream 66 k python3 aarch64 3.9.25-2.el9_7 baseos 26 k python3-libs aarch64 3.9.25-2.el9_7 baseos 8.1 M python3-pip-wheel noarch 21.3.1-1.el9 baseos 1.1 M python3-pyparsing noarch 2.4.7-9.el9 baseos 154 k python3-setuptools-wheel noarch 53.0.0-15.el9 baseos 468 k systemtap-sdt-devel aarch64 5.3-3.el9 appstream 69 k systemtap-sdt-dtrace aarch64 5.3-3.el9 appstream 70 k Transaction Summary ================================================================================ Install 56 Packages Total download size: 91 M Installed size: 294 M Downloading Packages: (1/56): htslib-1.23-1.el9.aarch64.rpm 19 MB/s | 542 kB 00:00 (2/56): htslib-devel-1.23-1.el9.aarch64.rpm 3.6 MB/s | 107 kB 00:00 (3/56): htslib-tools-1.23-1.el9.aarch64.rpm 20 MB/s | 715 kB 00:00 (4/56): libedit-3.1-38.20210216cvs.el9.aarch64. 945 kB/s | 105 kB 00:00 (5/56): python3-pyparsing-2.4.7-9.el9.noarch.rp 1.3 MB/s | 154 kB 00:00 (6/56): make-4.3-8.el9.aarch64.rpm 4.5 MB/s | 537 kB 00:00 (7/56): python3-pip-wheel-21.3.1-1.el9.noarch.r 11 MB/s | 1.1 MB 00:00 (8/56): libatomic-11.5.0-11.el9.aarch64.rpm 219 kB/s | 25 kB 00:00 (9/56): python3-setuptools-wheel-53.0.0-15.el9. 4.3 MB/s | 468 kB 00:00 (10/56): expat-2.5.0-5.el9_7.1.aarch64.rpm 1.4 MB/s | 112 kB 00:00 (11/56): python3-3.9.25-2.el9_7.aarch64.rpm 332 kB/s | 26 kB 00:00 (12/56): perl-Devel-PPPort-3.62-4.el9.aarch64.r 2.6 MB/s | 212 kB 00:00 (13/56): libmpc-1.2.1-4.el9.aarch64.rpm 868 kB/s | 66 kB 00:00 (14/56): perl-threads-2.25-460.el9.aarch64.rpm 580 kB/s | 60 kB 00:00 (15/56): perl-ExtUtils-MakeMaker-7.60-3.el9.noa 2.6 MB/s | 304 kB 00:00 (16/56): python3-libs-3.9.25-2.el9_7.aarch64.rp 27 MB/s | 8.1 MB 00:00 (17/56): perl-ExtUtils-Manifest-1.73-4.el9.noar 446 kB/s | 37 kB 00:00 (18/56): m4-1.4.19-1.el9.aarch64.rpm 2.3 MB/s | 301 kB 00:00 (19/56): perl-ExtUtils-ParseXS-3.40-460.el9.noa 1.7 MB/s | 190 kB 00:00 (20/56): perl-Test-Harness-3.42-461.el9.noarch. 3.6 MB/s | 299 kB 00:00 (21/56): perl-version-0.99.28-4.el9.aarch64.rpm 839 kB/s | 66 kB 00:00 (22/56): gsl-2.6-7.el9.aarch64.rpm 12 MB/s | 1.0 MB 00:00 (23/56): libxcrypt-devel-4.4.18-3.el9.aarch64.r 301 kB/s | 32 kB 00:00 (24/56): perl-ExtUtils-Command-7.60-3.el9.noarc 143 kB/s | 16 kB 00:00 (25/56): perl-ExtUtils-Install-2.20-4.el9.noarc 575 kB/s | 47 kB 00:00 (26/56): gsl-devel-2.6-7.el9.aarch64.rpm 5.5 MB/s | 652 kB 00:00 (27/56): perl-Thread-Queue-3.14-460.el9.noarch. 94 kB/s | 24 kB 00:00 (28/56): perl-threads-shared-1.61-460.el9.aarch 218 kB/s | 47 kB 00:00 (29/56): automake-1.16.2-8.el9.noarch.rpm 5.2 MB/s | 693 kB 00:00 (30/56): zlib-devel-1.2.11-40.el9.aarch64.rpm 382 kB/s | 47 kB 00:00 (31/56): perl-Benchmark-1.23-481.1.el9_6.noarch 257 kB/s | 26 kB 00:00 (32/56): perl-AutoSplit-5.74-481.1.el9_6.noarch 104 kB/s | 21 kB 00:00 (33/56): perl-DynaLoader-1.47-481.1.el9_6.aarch 216 kB/s | 25 kB 00:00 (34/56): perl-ExtUtils-Constant-0.25-481.1.el9_ 378 kB/s | 46 kB 00:00 (35/56): perl-ExtUtils-Embed-1.35-481.1.el9_6.n 147 kB/s | 17 kB 00:00 (36/56): perl-File-Compare-1.100.600-481.1.el9_ 143 kB/s | 13 kB 00:00 (37/56): perl-File-Copy-2.34-481.1.el9_6.noarch 232 kB/s | 20 kB 00:00 (38/56): perl-File-Find-1.37-481.1.el9_6.noarch 237 kB/s | 25 kB 00:00 (39/56): perl-FindBin-1.51-481.1.el9_6.noarch.r 128 kB/s | 14 kB 00:00 (40/56): perl-devel-5.32.1-481.1.el9_6.aarch64. 6.7 MB/s | 676 kB 00:00 (41/56): perl-lib-0.65-481.1.el9_6.aarch64.rpm 106 kB/s | 14 kB 00:00 (42/56): perl-locale-1.09-481.1.el9_6.noarch.rp 78 kB/s | 13 kB 00:00 (43/56): libubsan-11.5.0-11.el9.aarch64.rpm 1.4 MB/s | 175 kB 00:00 (44/56): systemtap-sdt-devel-5.3-3.el9.aarch64. 690 kB/s | 69 kB 00:00 (45/56): gcc-11.5.0-11.el9.aarch64.rpm 93 MB/s | 30 MB 00:00 (46/56): annobin-12.98-1.el9.aarch64.rpm 11 MB/s | 1.1 MB 00:00 (47/56): autoconf-2.69-41.el9.noarch.rpm 8.0 MB/s | 681 kB 00:00 (48/56): gcc-plugin-annobin-11.5.0-11.el9.aarch 438 kB/s | 36 kB 00:00 (49/56): emacs-filesystem-27.2-18.el9.noarch.rp 108 kB/s | 9.3 kB 00:00 (50/56): cpp-11.5.0-11.el9.aarch64.rpm 54 MB/s | 10 MB 00:00 (51/56): llvm-filesystem-20.1.8-3.el9.aarch64.r 104 kB/s | 9.1 kB 00:00 (52/56): libasan-11.5.0-11.el9.aarch64.rpm 4.3 MB/s | 399 kB 00:00 (53/56): systemtap-sdt-dtrace-5.3-3.el9.aarch64 896 kB/s | 70 kB 00:00 (54/56): glibc-devel-2.34-231.el9_7.2.aarch64.r 6.6 MB/s | 555 kB 00:00 (55/56): kernel-headers-5.14.0-611.26.1.el9_7.a 26 MB/s | 2.8 MB 00:00 (56/56): llvm-libs-20.1.8-3.el9.aarch64.rpm 93 MB/s | 28 MB 00:00 -------------------------------------------------------------------------------- Total 39 MB/s | 91 MB 00:02 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : perl-File-Find-1.37-481.1.el9_6.noarch 1/56 Installing : perl-File-Copy-2.34-481.1.el9_6.noarch 2/56 Installing : perl-File-Compare-1.100.600-481.1.el9_6.noarch 3/56 Installing : perl-DynaLoader-1.47-481.1.el9_6.aarch64 4/56 Installing : perl-ExtUtils-ParseXS-1:3.40-460.el9.noarch 5/56 Installing : perl-threads-1:2.25-460.el9.aarch64 6/56 Installing : libmpc-1.2.1-4.el9.aarch64 7/56 Installing : htslib-1.23-1.el9.aarch64 8/56 Installing : cpp-11.5.0-11.el9.aarch64 9/56 Installing : perl-threads-shared-1.61-460.el9.aarch64 10/56 Installing : perl-Thread-Queue-3.14-460.el9.noarch 11/56 Installing : perl-ExtUtils-Manifest-1:1.73-4.el9.noarch 12/56 Installing : perl-ExtUtils-Command-2:7.60-3.el9.noarch 13/56 Installing : kernel-headers-5.14.0-611.26.1.el9_7.aarch64 14/56 Installing : glibc-devel-2.34-231.el9_7.2.aarch64 15/56 Installing : libxcrypt-devel-4.4.18-3.el9.aarch64 16/56 Installing : llvm-filesystem-20.1.8-3.el9.aarch64 17/56 Installing : libasan-11.5.0-11.el9.aarch64 18/56 Installing : emacs-filesystem-1:27.2-18.el9.noarch 19/56 Installing : libubsan-11.5.0-11.el9.aarch64 20/56 Installing : perl-locale-1.09-481.1.el9_6.noarch 21/56 Installing : perl-version-7:0.99.28-4.el9.aarch64 22/56 Installing : perl-lib-0.65-481.1.el9_6.aarch64 23/56 Installing : perl-ExtUtils-Constant-0.25-481.1.el9_6.noarch 24/56 Installing : perl-Benchmark-1.23-481.1.el9_6.noarch 25/56 Installing : perl-Test-Harness-1:3.42-461.el9.noarch 26/56 Installing : perl-AutoSplit-5.74-481.1.el9_6.noarch 27/56 Installing : gsl-2.6-7.el9.aarch64 28/56 Installing : m4-1.4.19-1.el9.aarch64 29/56 Installing : autoconf-2.69-41.el9.noarch 30/56 Installing : automake-1.16.2-8.el9.noarch 31/56 Installing : perl-Devel-PPPort-3.62-4.el9.aarch64 32/56 Installing : expat-2.5.0-5.el9_7.1.aarch64 33/56 Installing : python3-setuptools-wheel-53.0.0-15.el9.noarch 34/56 Installing : libatomic-11.5.0-11.el9.aarch64 35/56 Installing : python3-pip-wheel-21.3.1-1.el9.noarch 36/56 Installing : python3-3.9.25-2.el9_7.aarch64 37/56 Installing : python3-libs-3.9.25-2.el9_7.aarch64 38/56 Installing : python3-pyparsing-2.4.7-9.el9.noarch 39/56 Installing : systemtap-sdt-dtrace-5.3-3.el9.aarch64 40/56 Installing : systemtap-sdt-devel-5.3-3.el9.aarch64 41/56 Installing : make-1:4.3-8.el9.aarch64 42/56 Installing : gcc-11.5.0-11.el9.aarch64 43/56 Running scriptlet: gcc-11.5.0-11.el9.aarch64 43/56 Installing : perl-ExtUtils-Install-2.20-4.el9.noarch 44/56 Installing : perl-devel-4:5.32.1-481.1.el9_6.aarch64 45/56 Installing : perl-ExtUtils-MakeMaker-2:7.60-3.el9.noarch 46/56 Installing : libedit-3.1-38.20210216cvs.el9.aarch64 47/56 Installing : llvm-libs-20.1.8-3.el9.aarch64 48/56 Installing : annobin-12.98-1.el9.aarch64 49/56 Running scriptlet: annobin-12.98-1.el9.aarch64 49/56 Installing : perl-ExtUtils-Embed-1.35-481.1.el9_6.noarch 50/56 Installing : gcc-plugin-annobin-11.5.0-11.el9.aarch64 51/56 Running scriptlet: gcc-plugin-annobin-11.5.0-11.el9.aarch64 51/56 Installing : gsl-devel-2.6-7.el9.aarch64 52/56 Installing : htslib-devel-1.23-1.el9.aarch64 53/56 Installing : htslib-tools-1.23-1.el9.aarch64 54/56 Installing : perl-FindBin-1.51-481.1.el9_6.noarch 55/56 Installing : zlib-devel-1.2.11-40.el9.aarch64 56/56 Running scriptlet: zlib-devel-1.2.11-40.el9.aarch64 56/56 Verifying : htslib-1.23-1.el9.aarch64 1/56 Verifying : htslib-devel-1.23-1.el9.aarch64 2/56 Verifying : htslib-tools-1.23-1.el9.aarch64 3/56 Verifying : python3-pyparsing-2.4.7-9.el9.noarch 4/56 Verifying : libedit-3.1-38.20210216cvs.el9.aarch64 5/56 Verifying : make-1:4.3-8.el9.aarch64 6/56 Verifying : python3-pip-wheel-21.3.1-1.el9.noarch 7/56 Verifying : libatomic-11.5.0-11.el9.aarch64 8/56 Verifying : python3-setuptools-wheel-53.0.0-15.el9.noarch 9/56 Verifying : expat-2.5.0-5.el9_7.1.aarch64 10/56 Verifying : python3-3.9.25-2.el9_7.aarch64 11/56 Verifying : python3-libs-3.9.25-2.el9_7.aarch64 12/56 Verifying : perl-Devel-PPPort-3.62-4.el9.aarch64 13/56 Verifying : libmpc-1.2.1-4.el9.aarch64 14/56 Verifying : perl-ExtUtils-MakeMaker-2:7.60-3.el9.noarch 15/56 Verifying : perl-threads-1:2.25-460.el9.aarch64 16/56 Verifying : m4-1.4.19-1.el9.aarch64 17/56 Verifying : perl-ExtUtils-Manifest-1:1.73-4.el9.noarch 18/56 Verifying : perl-ExtUtils-ParseXS-1:3.40-460.el9.noarch 19/56 Verifying : perl-Test-Harness-1:3.42-461.el9.noarch 20/56 Verifying : perl-version-7:0.99.28-4.el9.aarch64 21/56 Verifying : gsl-2.6-7.el9.aarch64 22/56 Verifying : libxcrypt-devel-4.4.18-3.el9.aarch64 23/56 Verifying : perl-ExtUtils-Command-2:7.60-3.el9.noarch 24/56 Verifying : perl-ExtUtils-Install-2.20-4.el9.noarch 25/56 Verifying : perl-Thread-Queue-3.14-460.el9.noarch 26/56 Verifying : perl-threads-shared-1.61-460.el9.aarch64 27/56 Verifying : gsl-devel-2.6-7.el9.aarch64 28/56 Verifying : automake-1.16.2-8.el9.noarch 29/56 Verifying : zlib-devel-1.2.11-40.el9.aarch64 30/56 Verifying : perl-AutoSplit-5.74-481.1.el9_6.noarch 31/56 Verifying : perl-Benchmark-1.23-481.1.el9_6.noarch 32/56 Verifying : perl-DynaLoader-1.47-481.1.el9_6.aarch64 33/56 Verifying : perl-ExtUtils-Constant-0.25-481.1.el9_6.noarch 34/56 Verifying : perl-ExtUtils-Embed-1.35-481.1.el9_6.noarch 35/56 Verifying : perl-File-Compare-1.100.600-481.1.el9_6.noarch 36/56 Verifying : perl-File-Copy-2.34-481.1.el9_6.noarch 37/56 Verifying : perl-File-Find-1.37-481.1.el9_6.noarch 38/56 Verifying : perl-FindBin-1.51-481.1.el9_6.noarch 39/56 Verifying : perl-devel-4:5.32.1-481.1.el9_6.aarch64 40/56 Verifying : perl-lib-0.65-481.1.el9_6.aarch64 41/56 Verifying : perl-locale-1.09-481.1.el9_6.noarch 42/56 Verifying : gcc-11.5.0-11.el9.aarch64 43/56 Verifying : libubsan-11.5.0-11.el9.aarch64 44/56 Verifying : systemtap-sdt-devel-5.3-3.el9.aarch64 45/56 Verifying : annobin-12.98-1.el9.aarch64 46/56 Verifying : autoconf-2.69-41.el9.noarch 47/56 Verifying : cpp-11.5.0-11.el9.aarch64 48/56 Verifying : emacs-filesystem-1:27.2-18.el9.noarch 49/56 Verifying : gcc-plugin-annobin-11.5.0-11.el9.aarch64 50/56 Verifying : libasan-11.5.0-11.el9.aarch64 51/56 Verifying : llvm-filesystem-20.1.8-3.el9.aarch64 52/56 Verifying : llvm-libs-20.1.8-3.el9.aarch64 53/56 Verifying : systemtap-sdt-dtrace-5.3-3.el9.aarch64 54/56 Verifying : glibc-devel-2.34-231.el9_7.2.aarch64 55/56 Verifying : kernel-headers-5.14.0-611.26.1.el9_7.aarch64 56/56 Installed products updated. Installed: annobin-12.98-1.el9.aarch64 autoconf-2.69-41.el9.noarch automake-1.16.2-8.el9.noarch cpp-11.5.0-11.el9.aarch64 emacs-filesystem-1:27.2-18.el9.noarch expat-2.5.0-5.el9_7.1.aarch64 gcc-11.5.0-11.el9.aarch64 gcc-plugin-annobin-11.5.0-11.el9.aarch64 glibc-devel-2.34-231.el9_7.2.aarch64 gsl-2.6-7.el9.aarch64 gsl-devel-2.6-7.el9.aarch64 htslib-1.23-1.el9.aarch64 htslib-devel-1.23-1.el9.aarch64 htslib-tools-1.23-1.el9.aarch64 kernel-headers-5.14.0-611.26.1.el9_7.aarch64 libasan-11.5.0-11.el9.aarch64 libatomic-11.5.0-11.el9.aarch64 libedit-3.1-38.20210216cvs.el9.aarch64 libmpc-1.2.1-4.el9.aarch64 libubsan-11.5.0-11.el9.aarch64 libxcrypt-devel-4.4.18-3.el9.aarch64 llvm-filesystem-20.1.8-3.el9.aarch64 llvm-libs-20.1.8-3.el9.aarch64 m4-1.4.19-1.el9.aarch64 make-1:4.3-8.el9.aarch64 perl-AutoSplit-5.74-481.1.el9_6.noarch perl-Benchmark-1.23-481.1.el9_6.noarch perl-Devel-PPPort-3.62-4.el9.aarch64 perl-DynaLoader-1.47-481.1.el9_6.aarch64 perl-ExtUtils-Command-2:7.60-3.el9.noarch perl-ExtUtils-Constant-0.25-481.1.el9_6.noarch perl-ExtUtils-Embed-1.35-481.1.el9_6.noarch perl-ExtUtils-Install-2.20-4.el9.noarch perl-ExtUtils-MakeMaker-2:7.60-3.el9.noarch perl-ExtUtils-Manifest-1:1.73-4.el9.noarch perl-ExtUtils-ParseXS-1:3.40-460.el9.noarch perl-File-Compare-1.100.600-481.1.el9_6.noarch perl-File-Copy-2.34-481.1.el9_6.noarch perl-File-Find-1.37-481.1.el9_6.noarch perl-FindBin-1.51-481.1.el9_6.noarch perl-Test-Harness-1:3.42-461.el9.noarch perl-Thread-Queue-3.14-460.el9.noarch perl-devel-4:5.32.1-481.1.el9_6.aarch64 perl-lib-0.65-481.1.el9_6.aarch64 perl-locale-1.09-481.1.el9_6.noarch perl-threads-1:2.25-460.el9.aarch64 perl-threads-shared-1.61-460.el9.aarch64 perl-version-7:0.99.28-4.el9.aarch64 python3-3.9.25-2.el9_7.aarch64 python3-libs-3.9.25-2.el9_7.aarch64 python3-pip-wheel-21.3.1-1.el9.noarch python3-pyparsing-2.4.7-9.el9.noarch python3-setuptools-wheel-53.0.0-15.el9.noarch systemtap-sdt-devel-5.3-3.el9.aarch64 systemtap-sdt-dtrace-5.3-3.el9.aarch64 zlib-devel-1.2.11-40.el9.aarch64 Complete! Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769385600 Wrote: /builddir/build/SRPMS/bcftools-1.23-1.el9.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 59 kB/s | 1.5 kB 00:00 Red Hat Enterprise Linux - BaseOS 43 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux - AppStream 30 kB/s | 4.5 kB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 37 kB/s | 4.5 kB 00:00 Extra Packages for Enterprise Linux 9 - aarch64 200 kB/s | 12 kB 00:00 Package autoconf-2.69-41.el9.noarch is already installed. Package automake-1.16.2-8.el9.noarch is already installed. Package gcc-11.5.0-11.el9.aarch64 is already installed. Package gsl-devel-2.6-7.el9.aarch64 is already installed. Package htslib-devel-1.23-1.el9.aarch64 is already installed. Package htslib-tools-1.23-1.el9.aarch64 is already installed. Package make-1:4.3-8.el9.aarch64 is already installed. Package perl-ExtUtils-Embed-1.35-481.1.el9_6.noarch is already installed. Package perl-File-Temp-1:0.231.100-4.el9.noarch is already installed. Package perl-FindBin-1.51-481.1.el9_6.noarch is already installed. Package perl-Getopt-Long-1:2.52-4.el9.noarch is already installed. Package perl-interpreter-4:5.32.1-481.1.el9_6.aarch64 is already installed. Package zlib-devel-1.2.11-40.el9.aarch64 is already installed. Dependencies resolved. Nothing to do. Complete! Finish: build setup for bcftools-1.23-1.el9.src.rpm Start: rpmbuild bcftools-1.23-1.el9.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769385600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.Dwg7mg + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bcftools-1.23 + /usr/bin/bzip2 -dc /builddir/build/SOURCES/bcftools-1.23.tar.bz2 + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd bcftools-1.23 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (bcftools-1.23-perl-fix-stray-errors-ldflags.patch):' Patch #0 (bcftools-1.23-perl-fix-stray-errors-ldflags.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file configure.ac + 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.vKGLXI + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.23 + autoreconf -fiv autoreconf: Entering directory `.' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level autoreconf: configure.ac: tracing configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level autoreconf: configure.ac: subdirectory $HTSDIR not present autoreconf: configure.ac: not using Libtool autoreconf: running: /usr/bin/autoconf --force configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level autoreconf: running: /usr/bin/autoheader --force configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level autoreconf: configure.ac: not using Automake autoreconf: Leaving directory `.' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./htslib-1.23/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./htslib-1.23/config.guess ++ basename ./htslib-1.23/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./htslib-1.23/config.guess '/usr/lib/rpm/redhat/config.guess' -> './htslib-1.23/config.guess' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./htslib-1.23/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./htslib-1.23/config.sub ++ basename ./htslib-1.23/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./htslib-1.23/config.sub '/usr/lib/rpm/redhat/config.sub' -> './htslib-1.23/config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh + ./configure --build=aarch64-redhat-linux-gnu --host=aarch64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' --prefix=/usr --with-htslib=system --enable-perl-filters --enable-libgsl '--with-bcf-plugin-path=/usr/local/libexec/bcftools:$(plugindir)' checking for aarch64-redhat-linux-gnu-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for gsl/gsl_version.h... yes checking for library containing cblas_dgemm... -lgslcblas checking for gsl_multifit_gradient in -lgsl... yes configure: removing -specs=...redhat-hardened... from Perl options 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 "1.23"' > version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o tabix.o tabix.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfindex.o vcfindex.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfisec.o vcfisec.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfquery.o vcfquery.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcffilter.o vcffilter.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfstats.o vcfstats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfsom.o vcfsom.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfgtcheck.o vcfgtcheck.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfview.o vcfview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfmerge.o vcfmerge.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfnorm.o vcfnorm.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfroh.o vcfroh.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfconcat.o vcfconcat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -c -o filter.o filter.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcmp.o vcmp.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfcall.o vcfcall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o gvcf.o gvcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o mcall.o mcall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfannotate.o vcfannotate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o tsv2vcf.o tsv2vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o reheader.o reheader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfhead.o vcfhead.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o HMM.o HMM.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfcnv.o vcfcnv.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfconvert.o vcfconvert.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bin.o bin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o ploidy.o ploidy.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o version.o version.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o hclust.o hclust.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o convert.o convert.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o smpl_ilist.o smpl_ilist.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o consensus.o consensus.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfbuf.o vcfbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o mpileup.o mpileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bam2bcf.o bam2bcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bam2bcf_iaux.o bam2bcf_iaux.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bam2bcf_edlib.o bam2bcf_edlib.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o read_consensus.o read_consensus.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bam_sample.o bam_sample.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o cols.o cols.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o dist.o dist.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o extsort.o extsort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfsort.o vcfsort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o ccall.o ccall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o csq.o csq.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o em.o em.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o kmin.o kmin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o str_finder.o str_finder.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o abuf.o abuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o prob1.o prob1.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o edlib.o edlib.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o mpileup2/mpileup.o mpileup2/mpileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o peakfit.o peakfit.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o polysomy.o polysomy.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o gff.o gff.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o test/test-rbuf.o test/test-rbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -DPLUGINPATH='"/usr/local/libexec/bcftools:/usr/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. 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-specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. 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-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/variant-distance.so version.c plugins/variant-distance.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -DUSE_GPL -c -o main.o main.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/vrfs.so version.c plugins/vrfs.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o plugins/vcf2table.so version.c plugins/vcf2table.c gcc -rdynamic -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o 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 bam2bcf_iaux.o bam2bcf_edlib.o read_consensus.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 gff.o edlib.o mpileup2/mpileup.o polysomy.o peakfit.o vcfplugin.o -lhts -lm -lz -lgsl -lgslcblas -Wl,--enable-new-dtags -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fstack-protector-strong -L/usr/local/lib -L/usr/lib64/perl5/CORE -lperl -lpthread -lresolv -ldl -lm -lcrypt -lutil -lc -lpthread lto-wrapper: warning: using serial compilation of 20 LTRANS jobs + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.lxCeSP + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64 ++ dirname /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64 + cd bcftools-1.23 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/bin /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/share/man/man1 /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools /usr/bin/install -p bcftools /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/bin /usr/bin/install -p misc/color-chrs.pl misc/gff2gff misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/roh-viz misc/run-roh.pl misc/vcfutils.pl misc/vrfs-variances /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/bin /usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/share/man/man1 /usr/bin/install -p plugins/*.so /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.23-1.el9 --unique-debug-suffix -1.23-1.el9.aarch64 --unique-debug-src-base bcftools-1.23-1.el9.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/bcftools-1.23 extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/bin/bcftools extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/GTsubset.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/GTisec.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/ad-bias.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/add-variantkey.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/af-dist.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/allele-length.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/check-ploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/check-sparsity.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/color-chrs.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/contrast.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/counts.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/dosage.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/fill-AN-AC.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/fill-from-fasta.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/fill-tags.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/fixploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/fixref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/frameshifts.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/guess-ploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/gvcfz.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/impute-info.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/indel-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/isecGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/mendelian2.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/missing2ref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/parental-origin.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/prune.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/remove-overlaps.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/scatter.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/setGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/smpl-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/split-vep.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/split.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/tag2tag.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/trio-dnm2.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/trio-switch-rate.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/trio-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/variant-distance.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/variantkey-hex.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/vcf2table.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/libexec/bcftools/vrfs.so original debug info size: 7128kB, size after compression: 6140kB /usr/bin/sepdebugcrcfix: Updated 42 CRC32s, 0 CRC32s did match. 6688 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/bin/vrfs-variances from /usr/bin/env perl to #!/usr/bin/perl mangling shebang in /usr/bin/roh-viz from /usr/bin/env perl to #!/usr/bin/perl mangling shebang in /usr/bin/gff2gff from /usr/bin/env perl to #!/usr/bin/perl Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.BU71Bz + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.23 + ldd bcftools + grep -E '/lib(64)?(/lp64d)?/libhts\.so\.' libhts.so.3 => /lib64/libhts.so.3 (0x0000ffffa6e89000) + 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/W_QOfA4kjq/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/W_QOfA4kjq/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/W_QOfA4kjq/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/W_QOfA4kjq/merge.a.bcf 1:3000151-3000151 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/W_QOfA4kjq/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/W_QOfA4kjq/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/W_QOfA4kjq/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/W_QOfA4kjq/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/W_QOfA4kjq/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/W_QOfA4kjq/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/W_QOfA4kjq/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/W_QOfA4kjq/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/W_QOfA4kjq/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/W_QOfA4kjq/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/W_QOfA4kjq/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/W_QOfA4kjq/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/W_QOfA4kjq/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/W_QOfA4kjq/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/W_QOfA4kjq/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/W_QOfA4kjq/idx.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/W_QOfA4kjq/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/W_QOfA4kjq/idx.bcf.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/W_QOfA4kjq/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/W_QOfA4kjq/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/W_QOfA4kjq/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/W_QOfA4kjq/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/W_QOfA4kjq/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/W_QOfA4kjq/empty.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/W_QOfA4kjq/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/W_QOfA4kjq/empty.bcf.csi .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.23/bcftools stats -s - /tmp/W_QOfA4kjq/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /builddir/build/BUILD/bcftools-1.23/misc/plot-vcfstats -m /tmp/W_QOfA4kjq/check.1.chk /tmp/W_QOfA4kjq/check.2.chk /tmp/W_QOfA4kjq/check.3.chk /tmp/W_QOfA4kjq/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-1.23/bcftools stats -s - /tmp/W_QOfA4kjq/stats.a.vcf.gz /tmp/W_QOfA4kjq/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.23/bcftools stats -s B /tmp/W_QOfA4kjq/stats.a.vcf.gz /tmp/W_QOfA4kjq/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.23/bcftools stats -s - /tmp/W_QOfA4kjq/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.23/bcftools stats -s - -i 'type="snp"' /tmp/W_QOfA4kjq/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.23/bcftools stats -s - /tmp/W_QOfA4kjq/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 -w 2 --no-version /tmp/W_QOfA4kjq/isec.match-id.1.1.vcf.gz /tmp/W_QOfA4kjq/isec.match-id.1.2.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 -w 2 -c id --no-version /tmp/W_QOfA4kjq/isec.match-id.1.1.vcf.gz /tmp/W_QOfA4kjq/isec.match-id.1.2.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 /tmp/W_QOfA4kjq/isec.a.vcf.gz /tmp/W_QOfA4kjq/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/W_QOfA4kjq/isec.a.vcf.gz /tmp/W_QOfA4kjq/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 -c both /tmp/W_QOfA4kjq/isec.a.vcf.gz /tmp/W_QOfA4kjq/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 -c any /tmp/W_QOfA4kjq/isec.a.vcf.gz /tmp/W_QOfA4kjq/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -C -c any /tmp/W_QOfA4kjq/isec.a.vcf.gz /tmp/W_QOfA4kjq/isec.b.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.23/bcftools isec --no-version -T /tmp/W_QOfA4kjq/isec.tab.gz /tmp/W_QOfA4kjq/isec.a.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.23/bcftools isec -Ob -T /tmp/W_QOfA4kjq/isec.tab.gz /tmp/W_QOfA4kjq/isec.a.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/W_QOfA4kjq/isec-miss.1.1.vcf.gz /tmp/W_QOfA4kjq/isec-miss.1.2.vcf.gz /tmp/W_QOfA4kjq/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -R /builddir/build/BUILD/bcftools-1.23/test/isec-miss.1.regs.txt -n +1 /tmp/W_QOfA4kjq/isec-miss.1.1.vcf.gz /tmp/W_QOfA4kjq/isec-miss.1.2.vcf.gz /tmp/W_QOfA4kjq/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/W_QOfA4kjq/isec-miss.2.1.vcf.gz /tmp/W_QOfA4kjq/isec-miss.2.2.vcf.gz /tmp/W_QOfA4kjq/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -R /builddir/build/BUILD/bcftools-1.23/test/isec-miss.1.regs.txt -n +1 /tmp/W_QOfA4kjq/isec-miss.2.1.vcf.gz /tmp/W_QOfA4kjq/isec-miss.2.2.vcf.gz /tmp/W_QOfA4kjq/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.broken-gvcf.a.vcf.gz /tmp/W_QOfA4kjq/merge.broken-gvcf.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.broken-gvcf.a.vcf.gz /tmp/W_QOfA4kjq/merge.broken-gvcf.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.broken-gvcf.a.bcf /tmp/W_QOfA4kjq/merge.broken-gvcf.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.broken-gvcf.a.bcf /tmp/W_QOfA4kjq/merge.broken-gvcf.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.symbolic.1.a.vcf.gz /tmp/W_QOfA4kjq/merge.symbolic.1.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.symbolic.1.a.vcf.gz /tmp/W_QOfA4kjq/merge.symbolic.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.symbolic.1.a.bcf /tmp/W_QOfA4kjq/merge.symbolic.1.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.symbolic.1.a.bcf /tmp/W_QOfA4kjq/merge.symbolic.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge none /tmp/W_QOfA4kjq/merge.multiallelics.1.a.vcf.gz /tmp/W_QOfA4kjq/merge.multiallelics.1.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge none /tmp/W_QOfA4kjq/merge.multiallelics.1.a.vcf.gz /tmp/W_QOfA4kjq/merge.multiallelics.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge none /tmp/W_QOfA4kjq/merge.multiallelics.1.a.bcf /tmp/W_QOfA4kjq/merge.multiallelics.1.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge none /tmp/W_QOfA4kjq/merge.multiallelics.1.a.bcf /tmp/W_QOfA4kjq/merge.multiallelics.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge both /tmp/W_QOfA4kjq/merge.multiallelics.1.a.vcf.gz /tmp/W_QOfA4kjq/merge.multiallelics.1.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge both /tmp/W_QOfA4kjq/merge.multiallelics.1.a.vcf.gz /tmp/W_QOfA4kjq/merge.multiallelics.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge both /tmp/W_QOfA4kjq/merge.multiallelics.1.a.bcf /tmp/W_QOfA4kjq/merge.multiallelics.1.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge both /tmp/W_QOfA4kjq/merge.multiallelics.1.a.bcf /tmp/W_QOfA4kjq/merge.multiallelics.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge none /tmp/W_QOfA4kjq/merge.12.a.vcf.gz /tmp/W_QOfA4kjq/merge.12.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge none /tmp/W_QOfA4kjq/merge.12.a.vcf.gz /tmp/W_QOfA4kjq/merge.12.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge none /tmp/W_QOfA4kjq/merge.12.a.bcf /tmp/W_QOfA4kjq/merge.12.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge none /tmp/W_QOfA4kjq/merge.12.a.bcf /tmp/W_QOfA4kjq/merge.12.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge both /tmp/W_QOfA4kjq/merge.12.a.vcf.gz /tmp/W_QOfA4kjq/merge.12.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge both /tmp/W_QOfA4kjq/merge.12.a.vcf.gz /tmp/W_QOfA4kjq/merge.12.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge both /tmp/W_QOfA4kjq/merge.12.a.bcf /tmp/W_QOfA4kjq/merge.12.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge both /tmp/W_QOfA4kjq/merge.12.a.bcf /tmp/W_QOfA4kjq/merge.12.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.phased.1.a.vcf.gz /tmp/W_QOfA4kjq/merge.phased.1.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.phased.1.a.vcf.gz /tmp/W_QOfA4kjq/merge.phased.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.phased.1.a.bcf /tmp/W_QOfA4kjq/merge.phased.1.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.phased.1.a.bcf /tmp/W_QOfA4kjq/merge.phased.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.11.a.vcf.gz /tmp/W_QOfA4kjq/merge.11.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.11.a.vcf.gz /tmp/W_QOfA4kjq/merge.11.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.11.a.bcf /tmp/W_QOfA4kjq/merge.11.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.11.a.bcf /tmp/W_QOfA4kjq/merge.11.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -i AF:join /tmp/W_QOfA4kjq/merge.join.a.vcf.gz /tmp/W_QOfA4kjq/merge.join.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AF:join /tmp/W_QOfA4kjq/merge.join.a.vcf.gz /tmp/W_QOfA4kjq/merge.join.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -i AF:join /tmp/W_QOfA4kjq/merge.join.a.bcf /tmp/W_QOfA4kjq/merge.join.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AF:join /tmp/W_QOfA4kjq/merge.join.a.bcf /tmp/W_QOfA4kjq/merge.join.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-single /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-single /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-single /tmp/W_QOfA4kjq/merge.LPL.a.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-single /tmp/W_QOfA4kjq/merge.LPL.a.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.b.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.b.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples /tmp/W_QOfA4kjq/merge.LPL.a.bcf /tmp/W_QOfA4kjq/merge.LPL.b.bcf /tmp/W_QOfA4kjq/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/W_QOfA4kjq/merge.LPL.a.bcf /tmp/W_QOfA4kjq/merge.LPL.b.bcf /tmp/W_QOfA4kjq/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 1 /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.b.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.b.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 1 /tmp/W_QOfA4kjq/merge.LPL.a.bcf /tmp/W_QOfA4kjq/merge.LPL.b.bcf /tmp/W_QOfA4kjq/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/W_QOfA4kjq/merge.LPL.a.bcf /tmp/W_QOfA4kjq/merge.LPL.b.bcf /tmp/W_QOfA4kjq/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 2 /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.b.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.b.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 2 /tmp/W_QOfA4kjq/merge.LPL.a.bcf /tmp/W_QOfA4kjq/merge.LPL.b.bcf /tmp/W_QOfA4kjq/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/W_QOfA4kjq/merge.LPL.a.bcf /tmp/W_QOfA4kjq/merge.LPL.b.bcf /tmp/W_QOfA4kjq/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 3 /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.b.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.b.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 3 /tmp/W_QOfA4kjq/merge.LPL.a.bcf /tmp/W_QOfA4kjq/merge.LPL.b.bcf /tmp/W_QOfA4kjq/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/W_QOfA4kjq/merge.LPL.a.bcf /tmp/W_QOfA4kjq/merge.LPL.b.bcf /tmp/W_QOfA4kjq/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 4 /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.b.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.b.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 4 /tmp/W_QOfA4kjq/merge.LPL.a.bcf /tmp/W_QOfA4kjq/merge.LPL.b.bcf /tmp/W_QOfA4kjq/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/W_QOfA4kjq/merge.LPL.a.bcf /tmp/W_QOfA4kjq/merge.LPL.b.bcf /tmp/W_QOfA4kjq/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 5 /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.b.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/W_QOfA4kjq/merge.LPL.a.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.b.vcf.gz /tmp/W_QOfA4kjq/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 5 /tmp/W_QOfA4kjq/merge.LPL.a.bcf /tmp/W_QOfA4kjq/merge.LPL.b.bcf /tmp/W_QOfA4kjq/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/W_QOfA4kjq/merge.LPL.a.bcf /tmp/W_QOfA4kjq/merge.LPL.b.bcf /tmp/W_QOfA4kjq/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples /tmp/W_QOfA4kjq/merge.a.vcf.gz /tmp/W_QOfA4kjq/merge.b.vcf.gz /tmp/W_QOfA4kjq/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/W_QOfA4kjq/merge.a.vcf.gz /tmp/W_QOfA4kjq/merge.b.vcf.gz /tmp/W_QOfA4kjq/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples /tmp/W_QOfA4kjq/merge.a.bcf /tmp/W_QOfA4kjq/merge.b.bcf /tmp/W_QOfA4kjq/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/W_QOfA4kjq/merge.a.bcf /tmp/W_QOfA4kjq/merge.b.bcf /tmp/W_QOfA4kjq/merge.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -Fx /tmp/W_QOfA4kjq/merge.a.vcf.gz /tmp/W_QOfA4kjq/merge.b.vcf.gz /tmp/W_QOfA4kjq/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -Fx /tmp/W_QOfA4kjq/merge.a.vcf.gz /tmp/W_QOfA4kjq/merge.b.vcf.gz /tmp/W_QOfA4kjq/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -Fx /tmp/W_QOfA4kjq/merge.a.bcf /tmp/W_QOfA4kjq/merge.b.bcf /tmp/W_QOfA4kjq/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -Fx /tmp/W_QOfA4kjq/merge.a.bcf /tmp/W_QOfA4kjq/merge.b.bcf /tmp/W_QOfA4kjq/merge.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -0 /tmp/W_QOfA4kjq/merge.a.vcf.gz /tmp/W_QOfA4kjq/merge.b.vcf.gz /tmp/W_QOfA4kjq/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -0 /tmp/W_QOfA4kjq/merge.a.vcf.gz /tmp/W_QOfA4kjq/merge.b.vcf.gz /tmp/W_QOfA4kjq/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -0 /tmp/W_QOfA4kjq/merge.a.bcf /tmp/W_QOfA4kjq/merge.b.bcf /tmp/W_QOfA4kjq/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -0 /tmp/W_QOfA4kjq/merge.a.bcf /tmp/W_QOfA4kjq/merge.b.bcf /tmp/W_QOfA4kjq/merge.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m none /tmp/W_QOfA4kjq/merge.2.a.vcf.gz /tmp/W_QOfA4kjq/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m none /tmp/W_QOfA4kjq/merge.2.a.vcf.gz /tmp/W_QOfA4kjq/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m none /tmp/W_QOfA4kjq/merge.2.a.bcf /tmp/W_QOfA4kjq/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m none /tmp/W_QOfA4kjq/merge.2.a.bcf /tmp/W_QOfA4kjq/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m both /tmp/W_QOfA4kjq/merge.2.a.vcf.gz /tmp/W_QOfA4kjq/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m both /tmp/W_QOfA4kjq/merge.2.a.vcf.gz /tmp/W_QOfA4kjq/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m both /tmp/W_QOfA4kjq/merge.2.a.bcf /tmp/W_QOfA4kjq/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m both /tmp/W_QOfA4kjq/merge.2.a.bcf /tmp/W_QOfA4kjq/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m all /tmp/W_QOfA4kjq/merge.2.a.vcf.gz /tmp/W_QOfA4kjq/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m all /tmp/W_QOfA4kjq/merge.2.a.vcf.gz /tmp/W_QOfA4kjq/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m all /tmp/W_QOfA4kjq/merge.2.a.bcf /tmp/W_QOfA4kjq/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m all /tmp/W_QOfA4kjq/merge.2.a.bcf /tmp/W_QOfA4kjq/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/W_QOfA4kjq/merge.3.a.vcf.gz /tmp/W_QOfA4kjq/merge.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/W_QOfA4kjq/merge.3.a.vcf.gz /tmp/W_QOfA4kjq/merge.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/W_QOfA4kjq/merge.3.a.bcf /tmp/W_QOfA4kjq/merge.3.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/W_QOfA4kjq/merge.3.a.bcf /tmp/W_QOfA4kjq/merge.3.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m id /tmp/W_QOfA4kjq/merge.4.a.vcf.gz /tmp/W_QOfA4kjq/merge.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m id /tmp/W_QOfA4kjq/merge.4.a.vcf.gz /tmp/W_QOfA4kjq/merge.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m id /tmp/W_QOfA4kjq/merge.4.a.bcf /tmp/W_QOfA4kjq/merge.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m id /tmp/W_QOfA4kjq/merge.4.a.bcf /tmp/W_QOfA4kjq/merge.4.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/gvcf.merge.1.vcf.gz /tmp/W_QOfA4kjq/gvcf.merge.2.vcf.gz /tmp/W_QOfA4kjq/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/gvcf.merge.1.vcf.gz /tmp/W_QOfA4kjq/gvcf.merge.2.vcf.gz /tmp/W_QOfA4kjq/gvcf.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/gvcf.merge.1.bcf /tmp/W_QOfA4kjq/gvcf.merge.2.bcf /tmp/W_QOfA4kjq/gvcf.merge.3.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/gvcf.merge.1.bcf /tmp/W_QOfA4kjq/gvcf.merge.2.bcf /tmp/W_QOfA4kjq/gvcf.merge.3.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.2.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.2.b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.2.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.2.b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - -m both,* /tmp/W_QOfA4kjq/merge.gvcf.2.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.2.b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/W_QOfA4kjq/merge.gvcf.2.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.2.b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - -m both,** /tmp/W_QOfA4kjq/merge.gvcf.2.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.2.b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/W_QOfA4kjq/merge.gvcf.2.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.2.b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - -i SRC:join /tmp/W_QOfA4kjq/merge.gvcf.3.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/W_QOfA4kjq/merge.gvcf.3.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.4.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.4.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.4.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.4.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.4.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.5.a.vcf.gz /tmp/W_QOfA4kjq/merge.5.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.5.a.vcf.gz /tmp/W_QOfA4kjq/merge.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.5.a.bcf /tmp/W_QOfA4kjq/merge.5.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.5.a.bcf /tmp/W_QOfA4kjq/merge.5.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.6.a.vcf.gz /tmp/W_QOfA4kjq/merge.6.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.6.a.vcf.gz /tmp/W_QOfA4kjq/merge.6.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.6.a.bcf /tmp/W_QOfA4kjq/merge.6.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.6.a.bcf /tmp/W_QOfA4kjq/merge.6.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.7.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.7.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.7.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.7.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.7.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.8.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.8.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.8.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.8.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.8.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples /tmp/W_QOfA4kjq/merge.7.a.vcf.gz /tmp/W_QOfA4kjq/merge.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/W_QOfA4kjq/merge.7.a.vcf.gz /tmp/W_QOfA4kjq/merge.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples /tmp/W_QOfA4kjq/merge.7.a.bcf /tmp/W_QOfA4kjq/merge.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/W_QOfA4kjq/merge.7.a.bcf /tmp/W_QOfA4kjq/merge.7.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/W_QOfA4kjq/merge.gvcf.9a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9c.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/W_QOfA4kjq/merge.gvcf.9a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9c.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/W_QOfA4kjq/merge.gvcf.9a.bcf /tmp/W_QOfA4kjq/merge.gvcf.9b.bcf /tmp/W_QOfA4kjq/merge.gvcf.9c.bcf /tmp/W_QOfA4kjq/merge.gvcf.9d.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/W_QOfA4kjq/merge.gvcf.9a.bcf /tmp/W_QOfA4kjq/merge.gvcf.9b.bcf /tmp/W_QOfA4kjq/merge.gvcf.9c.bcf /tmp/W_QOfA4kjq/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/W_QOfA4kjq/merge.gvcf.9a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9c.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/W_QOfA4kjq/merge.gvcf.9a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9c.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/W_QOfA4kjq/merge.gvcf.9a.bcf /tmp/W_QOfA4kjq/merge.gvcf.9b.bcf /tmp/W_QOfA4kjq/merge.gvcf.9c.bcf /tmp/W_QOfA4kjq/merge.gvcf.9d.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/W_QOfA4kjq/merge.gvcf.9a.bcf /tmp/W_QOfA4kjq/merge.gvcf.9b.bcf /tmp/W_QOfA4kjq/merge.gvcf.9c.bcf /tmp/W_QOfA4kjq/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/W_QOfA4kjq/merge.gvcf.9a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9c.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9d.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/W_QOfA4kjq/merge.gvcf.9a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9c.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9d.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/W_QOfA4kjq/merge.gvcf.9a.bcf /tmp/W_QOfA4kjq/merge.gvcf.9b.bcf /tmp/W_QOfA4kjq/merge.gvcf.9c.bcf /tmp/W_QOfA4kjq/merge.gvcf.9d.bcf /tmp/W_QOfA4kjq/merge.gvcf.9e.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/W_QOfA4kjq/merge.gvcf.9a.bcf /tmp/W_QOfA4kjq/merge.gvcf.9b.bcf /tmp/W_QOfA4kjq/merge.gvcf.9c.bcf /tmp/W_QOfA4kjq/merge.gvcf.9d.bcf /tmp/W_QOfA4kjq/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/W_QOfA4kjq/merge.gvcf.9a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9c.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9d.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/W_QOfA4kjq/merge.gvcf.9a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9c.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9d.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/W_QOfA4kjq/merge.gvcf.9a.bcf /tmp/W_QOfA4kjq/merge.gvcf.9b.bcf /tmp/W_QOfA4kjq/merge.gvcf.9c.bcf /tmp/W_QOfA4kjq/merge.gvcf.9d.bcf /tmp/W_QOfA4kjq/merge.gvcf.9e.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/W_QOfA4kjq/merge.gvcf.9a.bcf /tmp/W_QOfA4kjq/merge.gvcf.9b.bcf /tmp/W_QOfA4kjq/merge.gvcf.9c.bcf /tmp/W_QOfA4kjq/merge.gvcf.9d.bcf /tmp/W_QOfA4kjq/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.gvcf.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.gvcf.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.gvcf.10.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.gvcf.10.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m none /tmp/W_QOfA4kjq/merge.gvcf.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m none /tmp/W_QOfA4kjq/merge.gvcf.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m none /tmp/W_QOfA4kjq/merge.gvcf.10.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m none /tmp/W_QOfA4kjq/merge.gvcf.10.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa /tmp/W_QOfA4kjq/merge.gvcf.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa /tmp/W_QOfA4kjq/merge.gvcf.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa /tmp/W_QOfA4kjq/merge.gvcf.10.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa /tmp/W_QOfA4kjq/merge.gvcf.10.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa -m none /tmp/W_QOfA4kjq/merge.gvcf.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa -m none /tmp/W_QOfA4kjq/merge.gvcf.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa -m none /tmp/W_QOfA4kjq/merge.gvcf.10.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa -m none /tmp/W_QOfA4kjq/merge.gvcf.10.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.noidx.a.vcf.gz /tmp/W_QOfA4kjq/merge.noidx.b.vcf.gz /tmp/W_QOfA4kjq/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.noidx.a.vcf.gz /tmp/W_QOfA4kjq/merge.noidx.b.vcf.gz /tmp/W_QOfA4kjq/merge.noidx.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.noidx.a.bcf /tmp/W_QOfA4kjq/merge.noidx.b.bcf /tmp/W_QOfA4kjq/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.noidx.a.bcf /tmp/W_QOfA4kjq/merge.noidx.b.bcf /tmp/W_QOfA4kjq/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --no-index /builddir/build/BUILD/bcftools-1.23/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.23/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.23/test/merge.noidx.c.vcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --no-index /builddir/build/BUILD/bcftools-1.23/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.23/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.23/test/merge.noidx.c.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --no-index /tmp/W_QOfA4kjq/merge.noidx.a.bcf /tmp/W_QOfA4kjq/merge.noidx.b.bcf /tmp/W_QOfA4kjq/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --no-index /tmp/W_QOfA4kjq/merge.noidx.a.bcf /tmp/W_QOfA4kjq/merge.noidx.b.bcf /tmp/W_QOfA4kjq/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.8.a.vcf.gz /tmp/W_QOfA4kjq/merge.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.8.a.vcf.gz /tmp/W_QOfA4kjq/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.8.a.bcf /tmp/W_QOfA4kjq/merge.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.8.a.bcf /tmp/W_QOfA4kjq/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -i AN:sum,AC:sum /tmp/W_QOfA4kjq/merge.8.a.vcf.gz /tmp/W_QOfA4kjq/merge.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/W_QOfA4kjq/merge.8.a.vcf.gz /tmp/W_QOfA4kjq/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -i AN:sum,AC:sum /tmp/W_QOfA4kjq/merge.8.a.bcf /tmp/W_QOfA4kjq/merge.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/W_QOfA4kjq/merge.8.a.bcf /tmp/W_QOfA4kjq/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.9.a.vcf.gz /tmp/W_QOfA4kjq/merge.9.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.9.a.vcf.gz /tmp/W_QOfA4kjq/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/W_QOfA4kjq/merge.9.a.bcf /tmp/W_QOfA4kjq/merge.9.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/W_QOfA4kjq/merge.9.a.bcf /tmp/W_QOfA4kjq/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -i AN:sum,AC:sum /tmp/W_QOfA4kjq/merge.9.a.vcf.gz /tmp/W_QOfA4kjq/merge.9.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/W_QOfA4kjq/merge.9.a.vcf.gz /tmp/W_QOfA4kjq/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -i AN:sum,AC:sum /tmp/W_QOfA4kjq/merge.9.a.bcf /tmp/W_QOfA4kjq/merge.9.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/W_QOfA4kjq/merge.9.a.bcf /tmp/W_QOfA4kjq/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m none /tmp/W_QOfA4kjq/merge.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m none /tmp/W_QOfA4kjq/merge.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m none /tmp/W_QOfA4kjq/merge.10.a.bcf /tmp/W_QOfA4kjq/merge.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m none /tmp/W_QOfA4kjq/merge.10.a.bcf /tmp/W_QOfA4kjq/merge.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m both /tmp/W_QOfA4kjq/merge.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m both /tmp/W_QOfA4kjq/merge.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m both /tmp/W_QOfA4kjq/merge.10.a.bcf /tmp/W_QOfA4kjq/merge.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m both /tmp/W_QOfA4kjq/merge.10.a.bcf /tmp/W_QOfA4kjq/merge.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m snp-ins-del /tmp/W_QOfA4kjq/merge.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m snp-ins-del /tmp/W_QOfA4kjq/merge.10.a.vcf.gz /tmp/W_QOfA4kjq/merge.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m snp-ins-del /tmp/W_QOfA4kjq/merge.10.a.bcf /tmp/W_QOfA4kjq/merge.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m snp-ins-del /tmp/W_QOfA4kjq/merge.10.a.bcf /tmp/W_QOfA4kjq/merge.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/merge.mrules.1.a.vcf.gz /tmp/W_QOfA4kjq/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/merge.mrules.1.a.vcf.gz /tmp/W_QOfA4kjq/merge.mrules.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/merge.mrules.1.a.bcf /tmp/W_QOfA4kjq/merge.mrules.1.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/merge.mrules.1.a.bcf /tmp/W_QOfA4kjq/merge.mrules.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/W_QOfA4kjq/merge.mrules.1.a.vcf.gz /tmp/W_QOfA4kjq/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/W_QOfA4kjq/merge.mrules.1.a.vcf.gz /tmp/W_QOfA4kjq/merge.mrules.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/W_QOfA4kjq/merge.mrules.1.a.bcf /tmp/W_QOfA4kjq/merge.mrules.1.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/W_QOfA4kjq/merge.mrules.1.a.bcf /tmp/W_QOfA4kjq/merge.mrules.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.5.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.5.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.5.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.5.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.5.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - --merge none /tmp/W_QOfA4kjq/merge.gvcf.5.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/W_QOfA4kjq/merge.gvcf.5.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - --merge none /tmp/W_QOfA4kjq/merge.gvcf.5.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/W_QOfA4kjq/merge.gvcf.5.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.5.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.11.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.11.b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.11.a.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.11.b.vcf.gz /tmp/W_QOfA4kjq/merge.gvcf.11.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.11.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.11.b.bcf /tmp/W_QOfA4kjq/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/W_QOfA4kjq/merge.gvcf.11.a.bcf /tmp/W_QOfA4kjq/merge.gvcf.11.b.bcf /tmp/W_QOfA4kjq/merge.gvcf.11.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' /tmp/W_QOfA4kjq/smpl-count.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/smpl-count.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'smpl_count(LAA)==1' /tmp/W_QOfA4kjq/smpl-count.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/smpl-count.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'smpl_count(LAA)==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'smpl_count(LAA)==1 & GT="hom"' /tmp/W_QOfA4kjq/smpl-count.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/smpl-count.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'smpl_count(LAA)==1 & GT="hom"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'GT="hom" & smpl_count(LAA)==1' /tmp/W_QOfA4kjq/smpl-count.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/smpl-count.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'GT="hom" & smpl_count(LAA)==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]="."' /tmp/W_QOfA4kjq/query.filter.15.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.15.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]~"\."' /tmp/W_QOfA4kjq/query.filter.15.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.15.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]~"\."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]!="."' /tmp/W_QOfA4kjq/query.filter.15.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.15.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]!~"\."' /tmp/W_QOfA4kjq/query.filter.15.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.15.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]!~"\."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM %POS %ID %REF %ALT %QUAL %FILTER \t %INFO/CHROM %INFO/POS %INFO/ID %INFO/REF %INFO/ALT %INFO/QUAL %INFO/FILTER' /tmp/W_QOfA4kjq/query.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM %POS %ID %REF %ALT %QUAL %FILTER \t %INFO/CHROM %INFO/POS %INFO/ID %INFO/REF %INFO/ALT %INFO/QUAL %INFO/FILTER' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[ %CHROM] \t [ %POS] \t [ %ID] \t [ %REF] \t [ %ALT] \t [ %QUAL] \t [ %FILTER]' /tmp/W_QOfA4kjq/query.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[ %CHROM] \t [ %POS] \t [ %ID] \t [ %REF] \t [ %ALT] \t [ %QUAL] \t [ %FILTER]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[ %/CHROM] \t [ %/POS] \t [ %/ID] \t [ %/REF] \t [ %/ALT] \t [ %/QUAL] \t [ %/FILTER]' /tmp/W_QOfA4kjq/query.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[ %/CHROM] \t [ %/POS] \t [ %/ID] \t [ %/REF] \t [ %/ALT] \t [ %/QUAL] \t [ %/FILTER]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' /tmp/W_QOfA4kjq/query.filter.14.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.14.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="."' /tmp/W_QOfA4kjq/query.filter.14.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.14.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="0|1"' /tmp/W_QOfA4kjq/query.filter.14.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.14.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="0|1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t%INFO/AD\t%SUM(INFO/AD)' /tmp/W_QOfA4kjq/query.func.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.func.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t%INFO/AD\t%SUM(INFO/AD)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t[%AD ]\t%SUM(FORMAT/AD)' /tmp/W_QOfA4kjq/query.func.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.func.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t[%AD ]\t%SUM(FORMAT/AD)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %SUM(FORMAT/AD)]' /tmp/W_QOfA4kjq/query.func.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.func.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %SUM(FORMAT/AD)]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %sSUM(FORMAT/AD)]' /tmp/W_QOfA4kjq/query.func.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.func.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %sSUM(FORMAT/AD)]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/W_QOfA4kjq/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/W_QOfA4kjq/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/W_QOfA4kjq/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/builddir/build/BUILD/bcftools-1.23/test/query.string.2.1.txt' /tmp/W_QOfA4kjq/query.string.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.string.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/builddir/build/BUILD/bcftools-1.23/test/query.string.2.1.txt' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/builddir/build/BUILD/bcftools-1.23/test/query.string.2.2.txt' /tmp/W_QOfA4kjq/query.string.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.string.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/builddir/build/BUILD/bcftools-1.23/test/query.string.2.2.txt' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools query -f '%RSX\t%VKX\n' /tmp/W_QOfA4kjq/query.variantkey.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.variantkey.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/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/W_QOfA4kjq/view.vectors.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/W_QOfA4kjq/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/W_QOfA4kjq/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/W_QOfA4kjq/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/W_QOfA4kjq/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/W_QOfA4kjq/query.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/W_QOfA4kjq/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/W_QOfA4kjq/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/W_QOfA4kjq/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/W_QOfA4kjq/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%LINE' /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%LINE' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/W_QOfA4kjq/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/W_QOfA4kjq/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/W_QOfA4kjq/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/W_QOfA4kjq/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/W_QOfA4kjq/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/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/W_QOfA4kjq/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.23/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-1.23/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/W_QOfA4kjq/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/W_QOfA4kjq/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/W_QOfA4kjq/query.filter.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/W_QOfA4kjq/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/W_QOfA4kjq/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/W_QOfA4kjq/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/W_QOfA4kjq/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/W_QOfA4kjq/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/W_QOfA4kjq/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/W_QOfA4kjq/query.filter.4.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.4.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.23/test/query.56.out' /tmp/W_QOfA4kjq/view.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.23/test/query.56.out' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/W_QOfA4kjq/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/W_QOfA4kjq/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/W_QOfA4kjq/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/W_QOfA4kjq/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/W_QOfA4kjq/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/W_QOfA4kjq/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/W_QOfA4kjq/query.gtidx.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/W_QOfA4kjq/query.gtidx.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/W_QOfA4kjq/query.gtidx.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' /tmp/W_QOfA4kjq/query.gtidx.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/W_QOfA4kjq/query.gtidx.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/W_QOfA4kjq/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/W_QOfA4kjq/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/W_QOfA4kjq/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/W_QOfA4kjq/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/W_QOfA4kjq/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/W_QOfA4kjq/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/W_QOfA4kjq/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/W_QOfA4kjq/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' /tmp/W_QOfA4kjq/query.pbinom.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.pbinom.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/W_QOfA4kjq/query.filter.6.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.6.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/W_QOfA4kjq/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/W_QOfA4kjq/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/W_QOfA4kjq/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/W_QOfA4kjq/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/W_QOfA4kjq/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/W_QOfA4kjq/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/W_QOfA4kjq/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/W_QOfA4kjq/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/W_QOfA4kjq/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/W_QOfA4kjq/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/W_QOfA4kjq/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/W_QOfA4kjq/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/W_QOfA4kjq/query.filter.13.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.13.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/W_QOfA4kjq/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/W_QOfA4kjq/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/W_QOfA4kjq/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/W_QOfA4kjq/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/W_QOfA4kjq/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt /tmp/W_QOfA4kjq/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -l -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt /tmp/W_QOfA4kjq/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -l -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt /tmp/W_QOfA4kjq/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt /tmp/W_QOfA4kjq/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.txt /tmp/W_QOfA4kjq/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -l -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.txt /tmp/W_QOfA4kjq/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -l -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/W_QOfA4kjq/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/W_QOfA4kjq/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID="abc"' /tmp/W_QOfA4kjq/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID="abc"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID=@/builddir/build/BUILD/bcftools-1.23/test/query.filter.id.3.txt' /tmp/W_QOfA4kjq/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID=@/builddir/build/BUILD/bcftools-1.23/test/query.filter.id.3.txt' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID!="abc"' /tmp/W_QOfA4kjq/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID!="abc"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID!=@/builddir/build/BUILD/bcftools-1.23/test/query.filter.id.3.txt' /tmp/W_QOfA4kjq/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID!=@/builddir/build/BUILD/bcftools-1.23/test/query.filter.id.3.txt' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/W_QOfA4kjq/filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/W_QOfA4kjq/filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/W_QOfA4kjq/filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/W_QOfA4kjq/filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/W_QOfA4kjq/filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/W_QOfA4kjq/filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/W_QOfA4kjq/filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/W_QOfA4kjq/filter.13.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/filter.13.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/W_QOfA4kjq/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/W_QOfA4kjq/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/W_QOfA4kjq/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/W_QOfA4kjq/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/W_QOfA4kjq/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/W_QOfA4kjq/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/W_QOfA4kjq/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/W_QOfA4kjq/query.filter-or.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter-or.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' /tmp/W_QOfA4kjq/query.filter-or.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/query.filter-or.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s /tmp/W_QOfA4kjq/norm.check-ref.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.check-ref.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s /tmp/W_QOfA4kjq/norm.check-ref.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.check-ref.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both -i 'ID=@/builddir/build/BUILD/bcftools-1.23/test/norm.filter.txt' /tmp/W_QOfA4kjq/norm.filter.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both -i 'ID=@/builddir/build/BUILD/bcftools-1.23/test/norm.filter.txt' /tmp/W_QOfA4kjq/norm.filter.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both -i 'ALT!="C"' /tmp/W_QOfA4kjq/norm.filter.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both -i 'ALT!="C"' /tmp/W_QOfA4kjq/norm.filter.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both -i 'ID=@/builddir/build/BUILD/bcftools-1.23/test/norm.filter.txt' /tmp/W_QOfA4kjq/norm.filter.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both -i 'ID=@/builddir/build/BUILD/bcftools-1.23/test/norm.filter.txt' /tmp/W_QOfA4kjq/norm.filter.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both -i 'ALT!="C"' /tmp/W_QOfA4kjq/norm.filter.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both -i 'ALT!="C"' /tmp/W_QOfA4kjq/norm.filter.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c e /tmp/W_QOfA4kjq/norm.6.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.2.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c e /tmp/W_QOfA4kjq/norm.6.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.2.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.breakend.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.breakend.1.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.breakend.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.breakend.1.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.sort.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.sort.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - -S lex /tmp/W_QOfA4kjq/norm.sort.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - -S lex /tmp/W_QOfA4kjq/norm.sort.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/W_QOfA4kjq/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/W_QOfA4kjq/norm.join-missing-ploidy.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps . /tmp/W_QOfA4kjq/norm.split.5.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps . /tmp/W_QOfA4kjq/norm.split.5.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version /tmp/W_QOfA4kjq/norm.symbolic.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.symbolic.3.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version /tmp/W_QOfA4kjq/norm.symbolic.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.symbolic.3.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -cx /tmp/W_QOfA4kjq/norm.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -cx /tmp/W_QOfA4kjq/norm.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/W_QOfA4kjq/norm.split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/W_QOfA4kjq/norm.split.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/W_QOfA4kjq/norm.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/W_QOfA4kjq/norm.split.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- --force /tmp/W_QOfA4kjq/norm.split.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- --force /tmp/W_QOfA4kjq/norm.split.3.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/W_QOfA4kjq/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/W_QOfA4kjq/norm.split.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- --keep-sum AD /tmp/W_QOfA4kjq/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- --keep-sum AD /tmp/W_QOfA4kjq/norm.split.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/W_QOfA4kjq/norm.split.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/W_QOfA4kjq/norm.split.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/W_QOfA4kjq/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/W_QOfA4kjq/norm.merge.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/W_QOfA4kjq/norm.merge.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/W_QOfA4kjq/norm.merge.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/W_QOfA4kjq/norm.merge.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/W_QOfA4kjq/norm.merge.3.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ -s /tmp/W_QOfA4kjq/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ -s /tmp/W_QOfA4kjq/norm.merge.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -Nc s /tmp/W_QOfA4kjq/norm.setref.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -Nc s /tmp/W_QOfA4kjq/norm.setref.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version /tmp/W_QOfA4kjq/norm.telomere.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version /tmp/W_QOfA4kjq/norm.telomere.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d snps /tmp/W_QOfA4kjq/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d snps /tmp/W_QOfA4kjq/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d indels /tmp/W_QOfA4kjq/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d indels /tmp/W_QOfA4kjq/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both /tmp/W_QOfA4kjq/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both /tmp/W_QOfA4kjq/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d all /tmp/W_QOfA4kjq/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d all /tmp/W_QOfA4kjq/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d none /tmp/W_QOfA4kjq/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d none /tmp/W_QOfA4kjq/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/W_QOfA4kjq/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/W_QOfA4kjq/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d none /tmp/W_QOfA4kjq/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d none /tmp/W_QOfA4kjq/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/W_QOfA4kjq/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/W_QOfA4kjq/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d indels /tmp/W_QOfA4kjq/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d indels /tmp/W_QOfA4kjq/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d any /tmp/W_QOfA4kjq/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d any /tmp/W_QOfA4kjq/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both /tmp/W_QOfA4kjq/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both /tmp/W_QOfA4kjq/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d snps /tmp/W_QOfA4kjq/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d snps /tmp/W_QOfA4kjq/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/W_QOfA4kjq/norm.rmdup.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.rmdup.3.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/W_QOfA4kjq/norm.rmdup.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.rmdup.3.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d all /tmp/W_QOfA4kjq/norm.rmdup.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.rmdup.3.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d all /tmp/W_QOfA4kjq/norm.rmdup.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.rmdup.3.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s -a --old-rec-tag XX /tmp/W_QOfA4kjq/norm.2.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.2.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s -a --old-rec-tag XX /tmp/W_QOfA4kjq/norm.2.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.2.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s --old-rec-tag XX /tmp/W_QOfA4kjq/norm.iupac.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.iupac.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s --old-rec-tag XX /tmp/W_QOfA4kjq/norm.iupac.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.iupac.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s --old-rec-tag XX /tmp/W_QOfA4kjq/norm.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.3.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s --old-rec-tag XX /tmp/W_QOfA4kjq/norm.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.3.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s -i'alt="N"' --old-rec-tag XX /tmp/W_QOfA4kjq/norm.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.3.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s -i'alt="N"' --old-rec-tag XX /tmp/W_QOfA4kjq/norm.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.3.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any --force .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any --force -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/W_QOfA4kjq/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -a .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/W_QOfA4kjq/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -a -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/W_QOfA4kjq/atomize.split.1.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/W_QOfA4kjq/atomize.split.1.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.1.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.1.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.1.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.1.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . /tmp/W_QOfA4kjq/atomize.split.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . /tmp/W_QOfA4kjq/atomize.split.3.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/W_QOfA4kjq/atomize.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/W_QOfA4kjq/atomize.split.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/W_QOfA4kjq/atomize.split.5.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/W_QOfA4kjq/atomize.split.5.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.5.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/W_QOfA4kjq/atomize.split.5.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/W_QOfA4kjq/norm.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/W_QOfA4kjq/norm.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/W_QOfA4kjq/norm.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/W_QOfA4kjq/norm.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/W_QOfA4kjq/norm.5.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/W_QOfA4kjq/norm.5.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps . /tmp/W_QOfA4kjq/norm.5.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps . /tmp/W_QOfA4kjq/norm.5.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/W_QOfA4kjq/norm.m-any.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/W_QOfA4kjq/norm.m-any.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/W_QOfA4kjq/norm.phased-split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/W_QOfA4kjq/norm.phased-split.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/W_QOfA4kjq/norm.phased-join.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/W_QOfA4kjq/norm.phased-join.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI /tmp/W_QOfA4kjq/norm.symbolic.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.symbolic.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI /tmp/W_QOfA4kjq/norm.symbolic.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.symbolic.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI /tmp/W_QOfA4kjq/norm.symbolic.2.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.symbolic.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI /tmp/W_QOfA4kjq/norm.symbolic.2.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.symbolic.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI /tmp/W_QOfA4kjq/norm.right-align.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.right-align.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI /tmp/W_QOfA4kjq/norm.right-align.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.right-align.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI -g /builddir/build/BUILD/bcftools-1.23/test/norm.right-align.gff /tmp/W_QOfA4kjq/norm.right-align.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.right-align.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI -g /builddir/build/BUILD/bcftools-1.23/test/norm.right-align.gff /tmp/W_QOfA4kjq/norm.right-align.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.right-align.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/W_QOfA4kjq/norm.atom-split-norm.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.atom-split-norm.fa .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/W_QOfA4kjq/norm.atom-split-norm.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.atom-split-norm.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/W_QOfA4kjq/norm.string-tags.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/W_QOfA4kjq/norm.string-tags.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +indels .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +indels -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +snps -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +snps -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/W_QOfA4kjq/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - -i 'type="snp"' /tmp/W_QOfA4kjq/norm.split.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - -i 'type="snp"' /tmp/W_QOfA4kjq/norm.split.merge.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/W_QOfA4kjq/norm.merge.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/W_QOfA4kjq/norm.merge.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/W_QOfA4kjq/norm.merge.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/W_QOfA4kjq/norm.merge.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -i 'INFO/TAG=@/builddir/build/BUILD/bcftools-1.23/test/filter.string.1.txt' /tmp/W_QOfA4kjq/filter.string.1.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -i 'INFO/TAG=@/builddir/build/BUILD/bcftools-1.23/test/filter.string.1.txt' /tmp/W_QOfA4kjq/filter.string.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -i 'FMT/TAG=@/builddir/build/BUILD/bcftools-1.23/test/filter.string.1.txt' /tmp/W_QOfA4kjq/filter.string.1.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -i 'FMT/TAG=@/builddir/build/BUILD/bcftools-1.23/test/filter.string.1.txt' /tmp/W_QOfA4kjq/filter.string.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -HA /tmp/W_QOfA4kjq/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -HAA /tmp/W_QOfA4kjq/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r 1 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r 1:1-2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r 1:1,1:2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r 1:1-1 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1} | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1}:1-2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1}:1-1 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1-1} | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/weird-chr-names.vcf.gz -r {1:1-1}-2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok, expected non-zero status test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/W_QOfA4kjq/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/W_QOfA4kjq/view.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -f PASS -Xks NA00003 /tmp/W_QOfA4kjq/view.vcf.gz -r20,Y .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -f PASS -Xks NA00003 /tmp/W_QOfA4kjq/view.vcf.gz -r20,Y | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -xs NA00003 /tmp/W_QOfA4kjq/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -xs NA00003 /tmp/W_QOfA4kjq/view.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/W_QOfA4kjq/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/W_QOfA4kjq/view.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -p /tmp/W_QOfA4kjq/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -p /tmp/W_QOfA4kjq/view.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -P /tmp/W_QOfA4kjq/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -P /tmp/W_QOfA4kjq/view.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/W_QOfA4kjq/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/W_QOfA4kjq/view.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Hu /tmp/W_QOfA4kjq/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -GVsnps /tmp/W_QOfA4kjq/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -GVsnps /tmp/W_QOfA4kjq/view.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/W_QOfA4kjq/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/W_QOfA4kjq/view.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -s ^NA00003 /tmp/W_QOfA4kjq/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -s ^NA00003 /tmp/W_QOfA4kjq/view.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/W_QOfA4kjq/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -G /tmp/W_QOfA4kjq/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -G /tmp/W_QOfA4kjq/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -HG /tmp/W_QOfA4kjq/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -a /tmp/W_QOfA4kjq/many.alleles.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -a /tmp/W_QOfA4kjq/many.alleles.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -asA /tmp/W_QOfA4kjq/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -asA /tmp/W_QOfA4kjq/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -asB /tmp/W_QOfA4kjq/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -asB /tmp/W_QOfA4kjq/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -asA /tmp/W_QOfA4kjq/view.vectors.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -asA /tmp/W_QOfA4kjq/view.vectors.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i'TXT0="text"' /tmp/W_QOfA4kjq/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.23/test/view.chrs.tab /tmp/W_QOfA4kjq/view.chrs.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.23/test/view.chrs.tab /tmp/W_QOfA4kjq/view.chrs.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -i 'POS>=3062917' /tmp/W_QOfA4kjq/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -i 'POS>=3062917' /tmp/W_QOfA4kjq/filter.2.vcf.gz 1:3062917-3157410 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/W_QOfA4kjq/idx.1.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/W_QOfA4kjq/idx.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.23/test/idx.2.bed /tmp/W_QOfA4kjq/idx.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.23/test/idx.3.bed /tmp/W_QOfA4kjq/idx.3.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.23/test/idx.4.bed /tmp/W_QOfA4kjq/idx.4.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ht 2 /tmp/W_QOfA4kjq/view-t.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ht 3 /tmp/W_QOfA4kjq/view-t.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/W_QOfA4kjq/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/W_QOfA4kjq/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/W_QOfA4kjq/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/W_QOfA4kjq/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/W_QOfA4kjq/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/W_QOfA4kjq/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/W_QOfA4kjq/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/W_QOfA4kjq/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/W_QOfA4kjq/overlap.vcf.gz .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.1.vcf -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.2.vcf -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.4.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.4.vcf -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.5.vcf -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view -H .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -C5:nonmajor /tmp/W_QOfA4kjq/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -c6:nonmajor /tmp/W_QOfA4kjq/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -q0.3:major /tmp/W_QOfA4kjq/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/W_QOfA4kjq/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/W_QOfA4kjq/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/W_QOfA4kjq/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -a /tmp/W_QOfA4kjq/view-a.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.23/test/view.sites.txt /tmp/W_QOfA4kjq/view.sites.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.23/test/view.sites.txt /tmp/W_QOfA4kjq/view.sites.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.23/test/view.sites.txt.gz /tmp/W_QOfA4kjq/view.sites.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.23/test/view.sites.txt.gz /tmp/W_QOfA4kjq/view.sites.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.23/bcftools head /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.23/bcftools head -h 0 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.23/bcftools head -h 1 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.23/bcftools head -h 5 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.23/bcftools head -h 22 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.23/bcftools head -h 23 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.23/bcftools head -n 0 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.23/bcftools head -n 1 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.23/bcftools head -n 5 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.23/bcftools head -h 5 -n 5 < /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf .. ok test_vcf_head2: /builddir/build/BUILD/bcftools-1.23/bcftools head -s0 /tmp/W_QOfA4kjq/mpileup.2.vcf.gz .. ok test_vcf_head2: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ob /tmp/W_QOfA4kjq/mpileup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools head -s0 .. ok test_vcf_head2: /builddir/build/BUILD/bcftools-1.23/bcftools head -s1 /tmp/W_QOfA4kjq/mpileup.2.vcf.gz .. ok test_vcf_head2: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ob /tmp/W_QOfA4kjq/mpileup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools head -s1 .. ok test_vcf_head2: /builddir/build/BUILD/bcftools-1.23/bcftools head -s2 -h2 /tmp/W_QOfA4kjq/mpileup.2.vcf.gz .. ok test_vcf_head2: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ob /tmp/W_QOfA4kjq/mpileup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools head -s2 -h2 .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m -s sample1 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m -s sample1 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m -s ^sample2,sample3 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m -s ^sample2,sample3 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m -s sample3 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m -s sample3 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m -s ^sample1,sample2 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m -s ^sample1,sample2 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/call-ploidy.1.txt -S /builddir/build/BUILD/bcftools-1.23/test/call-ploidy.1.ped /builddir/build/BUILD/bcftools-1.23/test/call-ploidy.1.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/call-ploidy.1.txt -S /builddir/build/BUILD/bcftools-1.23/test/call-ploidy.1.ped /builddir/build/BUILD/bcftools-1.23/test/call-ploidy.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mg0 /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mg0 /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.ped /builddir/build/BUILD/bcftools-1.23/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.ped /builddir/build/BUILD/bcftools-1.23/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.23/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.23/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -G /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -G /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.4.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.23/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.23/test/mpileup.cals.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.23/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/W_QOfA4kjq/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.23/test/mpileup.cals.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -cv /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -cv /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.ped /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.ped /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.23/test/call-G.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.23/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/call-G.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.23/test/call-G.2.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.23/test/call-G.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'ALT="."' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'ALT="."' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.23/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.23/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.23/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.23/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="A"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="A"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="RR"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="RR"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="RA"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="RA"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="AR"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="AR"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="AA"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="AA"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="aA"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="aA"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="HET"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="HET"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.23/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.23/test/filter.7.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.23/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.23/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.23/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.23/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.23/bcftools sort -m 0 /builddir/build/BUILD/bcftools-1.23/test/sort.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.23/bcftools sort -Ob -m 0 /builddir/build/BUILD/bcftools-1.23/test/sort.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.23/bcftools sort -m 1000 /builddir/build/BUILD/bcftools-1.23/test/sort.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.23/bcftools sort -Ob -m 1000 /builddir/build/BUILD/bcftools-1.23/test/sort.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.23/test/regions.tab /tmp/W_QOfA4kjq/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.23/test/regions.tab .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /builddir/build/BUILD/bcftools-1.23/test/regions.tab /tmp/W_QOfA4kjq/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/W_QOfA4kjq/regions.tab.gz /tmp/W_QOfA4kjq/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/W_QOfA4kjq/regions.tab.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/W_QOfA4kjq/regions.tab.gz /tmp/W_QOfA4kjq/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/W_QOfA4kjq/regions.bed /tmp/W_QOfA4kjq/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/W_QOfA4kjq/regions.bed .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/W_QOfA4kjq/regions.bed /tmp/W_QOfA4kjq/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/W_QOfA4kjq/regions.bed.gz /tmp/W_QOfA4kjq/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/W_QOfA4kjq/regions.bed.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/W_QOfA4kjq/regions.bed.gz /tmp/W_QOfA4kjq/regions.vcf.gz .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots36.bed.gz -c CHROM,POS,-,~X,-,AF,-,-,- -i'SVTYPE={X}' -k /builddir/build/BUILD/bcftools-1.23/test/annotate36.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots36.bed.gz -c CHROM,POS,-,~X,-,AF,-,-,- -i'SVTYPE={X}' -k /builddir/build/BUILD/bcftools-1.23/test/annotate36.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots36.bed.gz -c CHROM,BEG,END,~X,-,AF,-,-,- -i'SVTYPE={X}' -k /builddir/build/BUILD/bcftools-1.23/test/annotate36.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots36.bed.gz -c CHROM,BEG,END,~X,-,AF,-,-,- -i'SVTYPE={X}' -k /builddir/build/BUILD/bcftools-1.23/test/annotate36.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots35.vcf.gz -c CHROM,POS,~ID,REF,ALT,INFO/src /tmp/W_QOfA4kjq/annotate35.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots35.vcf.gz -c CHROM,POS,~ID,REF,ALT,INFO/src /tmp/W_QOfA4kjq/annotate35.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /builddir/build/BUILD/bcftools-1.23/test/annotate.escape.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /builddir/build/BUILD/bcftools-1.23/test/annotate.escape.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /builddir/build/BUILD/bcftools-1.23/test/annotate.match.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /builddir/build/BUILD/bcftools-1.23/test/annotate.match.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /builddir/build/BUILD/bcftools-1.23/test/annotate.match.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /builddir/build/BUILD/bcftools-1.23/test/annotate.match.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /builddir/build/BUILD/bcftools-1.23/test/annotate.match.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /builddir/build/BUILD/bcftools-1.23/test/annotate.match.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/W_QOfA4kjq/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/W_QOfA4kjq/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.23/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.23/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -x FORMAT /builddir/build/BUILD/bcftools-1.23/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -x FORMAT /builddir/build/BUILD/bcftools-1.23/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots4.vcf.gz -c +INFO /tmp/W_QOfA4kjq/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots4.vcf.gz -c +INFO /tmp/W_QOfA4kjq/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.23/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.23/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.23/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.23/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.23/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.23/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots11.vcf.gz -c FMT /tmp/W_QOfA4kjq/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots11.vcf.gz -c FMT /tmp/W_QOfA4kjq/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c FMT/newGT:=GT /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots2.vcf.gz -c FMT/newGT:=GT /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots12.vcf.gz -c FMT/GT:=newGT /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots12.vcf.gz -c FMT/GT:=newGT /tmp/W_QOfA4kjq/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.23/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.23/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.23/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.23/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.23/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.23/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.23/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.23/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.23/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.23/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.23/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.23/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /builddir/build/BUILD/bcftools-1.23/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /builddir/build/BUILD/bcftools-1.23/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -x FILTER /builddir/build/BUILD/bcftools-1.23/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -x FILTER /builddir/build/BUILD/bcftools-1.23/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.23/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.23/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.23/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.23/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.23/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.23/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/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-1.23/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/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-1.23/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/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-1.23/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/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-1.23/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -c INFO/FILTER:=FILTER /builddir/build/BUILD/bcftools-1.23/test/annotate19.dst.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -c INFO/FILTER:=FILTER /builddir/build/BUILD/bcftools-1.23/test/annotate19.dst.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/W_QOfA4kjq/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate20.src.vcf.gz -c FMT/GT /tmp/W_QOfA4kjq/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate20.src.vcf.gz -c FMT/GT /tmp/W_QOfA4kjq/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate20.src.vcf.gz -c +FMT/GT /tmp/W_QOfA4kjq/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate20.src.vcf.gz -c +FMT/GT /tmp/W_QOfA4kjq/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate20.src.vcf.gz -c -FMT/GT /tmp/W_QOfA4kjq/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate20.src.vcf.gz -c -FMT/GT /tmp/W_QOfA4kjq/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.23/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.23/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/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-1.23/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/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-1.23/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.23/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.23/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate --rename-annots /builddir/build/BUILD/bcftools-1.23/test/annotate21.txt /builddir/build/BUILD/bcftools-1.23/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob --rename-annots /builddir/build/BUILD/bcftools-1.23/test/annotate21.txt /builddir/build/BUILD/bcftools-1.23/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/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-1.23/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/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-1.23/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/W_QOfA4kjq/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/W_QOfA4kjq/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.23/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.23/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate24.src.vcf.gz -c XX /tmp/W_QOfA4kjq/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate24.src.vcf.gz -c XX /tmp/W_QOfA4kjq/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.23/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.23/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate26.tab.gz -c CHROM,POS,-POS /builddir/build/BUILD/bcftools-1.23/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate26.tab.gz -c CHROM,POS,-POS /builddir/build/BUILD/bcftools-1.23/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.23/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.23/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /builddir/build/BUILD/bcftools-1.23/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /builddir/build/BUILD/bcftools-1.23/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots.id.vcf.gz -c ALT /tmp/W_QOfA4kjq/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots.id.vcf.gz -c ALT /tmp/W_QOfA4kjq/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots.id.vcf.gz -c +ALT /tmp/W_QOfA4kjq/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots.id.vcf.gz -c +ALT /tmp/W_QOfA4kjq/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/W_QOfA4kjq/annotate.id.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/W_QOfA4kjq/annotate.id.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/W_QOfA4kjq/annotate.id.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/W_QOfA4kjq/annotate.id.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /builddir/build/BUILD/bcftools-1.23/test/annotate27.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /builddir/build/BUILD/bcftools-1.23/test/annotate27.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -m XXX /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -m XXX /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /builddir/build/BUILD/bcftools-1.23/test/annotate34.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /builddir/build/BUILD/bcftools-1.23/test/annotate34.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/W_QOfA4kjq/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /builddir/build/BUILD/bcftools-1.23/test/annots-mark.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/W_QOfA4kjq/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /builddir/build/BUILD/bcftools-1.23/test/annots-mark.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +check-ploidy --no-version /tmp/W_QOfA4kjq/checkploidy.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +check-ploidy --no-version /tmp/W_QOfA4kjq/checkploidy.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +check-ploidy --no-version /tmp/W_QOfA4kjq/checkploidy.2.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +check-ploidy --no-version /tmp/W_QOfA4kjq/checkploidy.2.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +check-ploidy --no-version /tmp/W_QOfA4kjq/checkploidy.2.vcf.gz -- -m | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +check-ploidy --no-version /tmp/W_QOfA4kjq/checkploidy.2.bcf -- -m | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +missing2ref --no-version /tmp/W_QOfA4kjq/plugin1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +missing2ref --no-version /tmp/W_QOfA4kjq/plugin1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/plugin1.vcf.gz -- -t . -n 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/plugin1.bcf -- -t . -n 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.23/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.23/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.23/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.23/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.23/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.23/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.2.vcf.gz -- -t a -n i | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.2.bcf -- -t a -n i | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.vcf.gz -- -t a -n pM | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.bcf -- -t a -n pM | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.vcf.gz -- -t a -n pm | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.bcf -- -t a -n pm | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.vcf.gz -- -t a -n c:1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.bcf -- -t a -n c:1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.vcf.gz -- -t a -n c:"1|1" | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.bcf -- -t a -n c:"1|1" | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.vcf.gz -- -t a -n c:"m|M" | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.bcf -- -t a -n c:"m|M" | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.vcf.gz -- -t a -n c:0/1/1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.bcf -- -t a -n c:0/1/1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.vcf.gz -i 'GT="mis"' -- -t . -nc:././. | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.3.bcf -i 'GT="mis"' -- -t . -nc:././. | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.4.bcf -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.4.bcf -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.5.vcf.gz -- -t a -n X | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] AD should be declared as Number=R [W::bcf_hdr_check_sanity] AD should be declared as Number=R test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.5.bcf -- -t a -n X | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.5.vcf.gz -- -t a -n c:0/X/X | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] AD should be declared as Number=R [W::bcf_hdr_check_sanity] AD should be declared as Number=R test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.5.bcf -- -t a -n c:0/X/X | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.6.vcf.gz -- -t ./x -n . | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.6.bcf -- -t ./x -n . | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.6.vcf.gz -- -t . -n . | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.6.bcf -- -t . -n . | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.6.vcf.gz -- -t r:0.5 -n . | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/W_QOfA4kjq/setGT.6.bcf -- -t r:0.5 -n . | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-AN-AC --no-version /tmp/W_QOfA4kjq/plugin1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-AN-AC --no-version /tmp/W_QOfA4kjq/plugin1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +dosage /tmp/W_QOfA4kjq/dosage.vcf.gz -- -t PL | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +dosage /tmp/W_QOfA4kjq/dosage.bcf -- -t PL | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +dosage /tmp/W_QOfA4kjq/dosage.vcf.gz -- -t GL | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +dosage /tmp/W_QOfA4kjq/dosage.bcf -- -t GL | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +dosage /tmp/W_QOfA4kjq/dosage.vcf.gz -- -t GT | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +dosage /tmp/W_QOfA4kjq/dosage.bcf -- -t GT | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixploidy --no-version /tmp/W_QOfA4kjq/fixploidy.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.23/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.23/test/fixploidy.ploidy | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixploidy --no-version /tmp/W_QOfA4kjq/fixploidy.bcf -- -s /builddir/build/BUILD/bcftools-1.23/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.23/test/fixploidy.ploidy | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +guess-ploidy /tmp/W_QOfA4kjq/view.PL.vcf.gz -v -rX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +guess-ploidy /tmp/W_QOfA4kjq/view.PL.bcf -v -rX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +guess-ploidy /tmp/W_QOfA4kjq/view.GL.vcf.gz -v -rX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +guess-ploidy /tmp/W_QOfA4kjq/view.GL.bcf -v -rX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/W_QOfA4kjq/view.GL.vcf.gz -- -r --gl-to-pl | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/W_QOfA4kjq/view.GL.bcf -- -r --gl-to-pl | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/W_QOfA4kjq/view.GL.vcf.gz -- --gl-to-gp | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/W_QOfA4kjq/view.GL.bcf -- --gl-to-gp | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/W_QOfA4kjq/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/W_QOfA4kjq/view.GP.bcf -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/W_QOfA4kjq/tag2tag.LPL.1.vcf.gz -- --LXX-to-XX | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/W_QOfA4kjq/tag2tag.LPL.1.bcf -- --LXX-to-XX | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/W_QOfA4kjq/tag2tag.LPL.1.vcf.gz -- --LXX-to-XX -r | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/W_QOfA4kjq/tag2tag.LPL.1.bcf -- --LXX-to-XX -r | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/W_QOfA4kjq/tag2tag.LPL.1.vcf.gz -- --LXX-to-XX -r -d AD:0,PL:255 -s 3 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/W_QOfA4kjq/tag2tag.LPL.1.bcf -- --LXX-to-XX -r -d AD:0,PL:255 -s 3 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +add-variantkey /tmp/W_QOfA4kjq/query.variantkey.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +add-variantkey /tmp/W_QOfA4kjq/query.variantkey.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variantkey-hex /tmp/W_QOfA4kjq/query.variantkey.vcf.gz test/ | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variantkey-hex /tmp/W_QOfA4kjq/query.variantkey.bcf test/ | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +allele-length /tmp/W_QOfA4kjq/query.nucleotide.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +allele-length /tmp/W_QOfA4kjq/query.nucleotide.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/query.func.1.vcf.gz -- -t 'FMT/AB:1=float(FMT/AD[*:0] / ssum(FMT/AD[*]))' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/query.func.1.bcf -- -t 'FMT/AB:1=float(FMT/AD[*:0] / ssum(FMT/AD[*]))' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fmissing.vcf.gz -- -S /builddir/build/BUILD/bcftools-1.23/test/fmissing.txt -t 'F_MISSING' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fmissing.bcf -- -S /builddir/build/BUILD/bcftools-1.23/test/fmissing.txt -t 'F_MISSING' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fmissing.vcf.gz -- -S /builddir/build/BUILD/bcftools-1.23/test/fmissing.txt -t 'F_MISSING:1=F_PASS(GT="mis")' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fmissing.bcf -- -S /builddir/build/BUILD/bcftools-1.23/test/fmissing.txt -t 'F_MISSING:1=F_PASS(GT="mis")' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fmissing.vcf.gz -- -S /builddir/build/BUILD/bcftools-1.23/test/fmissing.txt -t 'N_MISSING:1=int(N_PASS(GT="mis"))' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fmissing.bcf -- -S /builddir/build/BUILD/bcftools-1.23/test/fmissing.txt -t 'N_MISSING:1=int(N_PASS(GT="mis"))' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fisher.vcf.gz -- -t 'FT:1=phred(fisher(INFO/DP4))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fisher.bcf -- -t 'FT:1=phred(fisher(INFO/DP4))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fisher.vcf.gz -- -t 'FT:1=phred(fisher(INFO/ADF[0,2],INFO/ADR[0,2]))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fisher.bcf -- -t 'FT:1=phred(fisher(INFO/ADF[0,2],INFO/ADR[0,2]))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fisher.vcf.gz -- -t 'FT:1=phred(fisher(INFO/ADF,INFO/ADR))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fisher.bcf -- -t 'FT:1=phred(fisher(INFO/ADF,INFO/ADR))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fisher.vcf.gz -- -t 'FMT/FT:1=phred(fisher(FMT/DP4))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fisher.bcf -- -t 'FMT/FT:1=phred(fisher(FMT/DP4))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fisher.vcf.gz -- -t 'FMT/FT:1=phred(fisher(FORMAT/ADF,FORMAT/ADR))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fisher.bcf -- -t 'FMT/FT:1=phred(fisher(FORMAT/ADF,FORMAT/ADR))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fisher.vcf.gz -- -t 'FMT/FT:1=phred(fisher(FORMAT/ADF[:0,1],FORMAT/ADR[:0,1]))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fisher.bcf -- -t 'FMT/FT:1=phred(fisher(FORMAT/ADF[:0,1],FORMAT/ADR[:0,1]))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/view.vcf.gz -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/view.bcf -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/view.vcf.gz -- -t AC -S /builddir/build/BUILD/bcftools-1.23/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/view.bcf -- -t AC -S /builddir/build/BUILD/bcftools-1.23/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/view.vcf.gz -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.23/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/view.bcf -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.23/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/many-alts.vcf.gz -- -t AN,AC | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/many-alts.bcf -- -t AN,AC | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-hemi.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-hemi.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-hemi.vcf.gz -- -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-hemi.bcf -- -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-hwe.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-hwe.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-hwe.vcf.gz -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-hwe.bcf -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-rw.vcf.gz -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-rw.bcf -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-AN0.vcf.gz -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-AN0.bcf -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-VAF.vcf.gz -- -t VAF,VAF1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-VAF.bcf -- -t VAF,VAF1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-AD.vcf.gz -- -t 'FORMAT/DP:1=int(smpl_sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-AD.bcf -- -t 'FORMAT/DP:1=int(smpl_sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-AD.vcf.gz -- -t 'good=N_PASS(binom(FMT/AD[:0],FMT/AD[:1])>=1e-5)','bad=N_PASS(binom(FMT/AD[:0],FMT/AD[:1])<1e-5)' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/W_QOfA4kjq/fill-tags-AD.bcf -- -t 'good=N_PASS(binom(FMT/AD[:0],FMT/AD[:1])>=1e-5)','bad=N_PASS(binom(FMT/AD[:0],FMT/AD[:1])<1e-5)' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.vcf.gz | grep -v bcftools | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.bcf | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.vcf.gz -- -H | grep -v bcftools | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.bcf -- -H | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.vcf.gz -- -Hm | grep -v bcftools | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.bcf -- -Hm | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.vcf.gz -- -Hmv | grep -v bcftools | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.bcf -- -Hmv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.vcf.gz -- -Hv | grep -v bcftools | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.bcf -- -Hv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.vcf.gz -- -m | grep -v bcftools | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.bcf -- -m | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.vcf.gz -- -mv | grep -v bcftools | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.bcf -- -mv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.vcf.gz -- -v | grep -v bcftools | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/W_QOfA4kjq/view.bcf -- -v | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-switch-rate /tmp/W_QOfA4kjq/trio.vcf.gz -- -p /builddir/build/BUILD/bcftools-1.23/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-switch-rate /tmp/W_QOfA4kjq/trio.bcf -- -p /builddir/build/BUILD/bcftools-1.23/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-stats /tmp/W_QOfA4kjq/trio-stats.vcf.gz -a 1 -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-stats /tmp/W_QOfA4kjq/trio-stats.bcf -a 1 -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-stats /tmp/W_QOfA4kjq/trio-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-stats /tmp/W_QOfA4kjq/trio-stats.bcf -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +smpl-stats /tmp/W_QOfA4kjq/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +smpl-stats /tmp/W_QOfA4kjq/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +indel-stats /tmp/W_QOfA4kjq/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +indel-stats /tmp/W_QOfA4kjq/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +indel-stats /tmp/W_QOfA4kjq/indel-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +indel-stats /tmp/W_QOfA4kjq/indel-stats.bcf -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +indel-stats /tmp/W_QOfA4kjq/indel-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +indel-stats /tmp/W_QOfA4kjq/indel-stats.bcf -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/W_QOfA4kjq/ad-bias.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/W_QOfA4kjq/ad-bias.bcf -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/W_QOfA4kjq/ad-bias.2.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/W_QOfA4kjq/ad-bias.2.bcf -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/W_QOfA4kjq/ad-bias.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/W_QOfA4kjq/ad-bias.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/W_QOfA4kjq/ad-bias.2.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/W_QOfA4kjq/ad-bias.2.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +af-dist /tmp/W_QOfA4kjq/af-dist.vcf.gz | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +af-dist /tmp/W_QOfA4kjq/af-dist.bcf | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/W_QOfA4kjq/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -i /tmp/W_QOfA4kjq/fixref.2b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/W_QOfA4kjq/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -i /tmp/W_QOfA4kjq/fixref.2b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/W_QOfA4kjq/fixref.3.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/fixref.3.fa -m top | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/W_QOfA4kjq/fixref.3.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/fixref.3.fa -m top | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/W_QOfA4kjq/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m ref-alt | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/W_QOfA4kjq/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m ref-alt | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/W_QOfA4kjq/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m flip | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/W_QOfA4kjq/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m flip | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/W_QOfA4kjq/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m flip-all | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/W_QOfA4kjq/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m flip-all | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/W_QOfA4kjq/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m swap | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/W_QOfA4kjq/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m swap | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-from-fasta /tmp/W_QOfA4kjq/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.23/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-from-fasta /tmp/W_QOfA4kjq/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.23/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-from-fasta /tmp/W_QOfA4kjq/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/aa.fa -c REF -N | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-from-fasta /tmp/W_QOfA4kjq/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/aa.fa -c REF -N | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-from-fasta /tmp/W_QOfA4kjq/ref.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -c REF | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-from-fasta /tmp/W_QOfA4kjq/ref.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -c REF | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTsubset --no-version /tmp/W_QOfA4kjq/view.vcf.gz -- -s NA00001 | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTsubset --no-version /tmp/W_QOfA4kjq/view.bcf -- -s NA00001 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTsubset --no-version /tmp/W_QOfA4kjq/view.vcf.gz -- -s NA00001,NA00002 | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTsubset --no-version /tmp/W_QOfA4kjq/view.bcf -- -s NA00001,NA00002 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTsubset --no-version /tmp/W_QOfA4kjq/view.vcf.gz -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_ .. ok [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float [W::bcf_hdr_check_sanity] MQ should be declared as Type=Float test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTsubset --no-version /tmp/W_QOfA4kjq/view.bcf -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/W_QOfA4kjq/mendelian.vcf.gz -p child1,dad1,mom1 -md | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/W_QOfA4kjq/mendelian.bcf -p child1,dad1,mom1 -md | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/W_QOfA4kjq/mendelian.vcf.gz -p child1,dad1,mom1 -mg | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/W_QOfA4kjq/mendelian.bcf -p child1,dad1,mom1 -mg | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/W_QOfA4kjq/mendelian.vcf.gz -p child1,dad1,mom1 -me | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/W_QOfA4kjq/mendelian.bcf -p child1,dad1,mom1 -me | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/W_QOfA4kjq/mendelian.vcf.gz -p child1,dad1,mom1 -ma | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/W_QOfA4kjq/mendelian.bcf -p child1,dad1,mom1 -ma | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/W_QOfA4kjq/mendelian.vcf.gz -p child1,dad1,mom1 -mm | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/W_QOfA4kjq/mendelian.bcf -p child1,dad1,mom1 -mm | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/W_QOfA4kjq/mendelian.vcf.gz -p child1,dad1,mom1 | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/W_QOfA4kjq/mendelian.bcf -p child1,dad1,mom1 | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/W_QOfA4kjq/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/W_QOfA4kjq/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/W_QOfA4kjq/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.23/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.23/test/contrast1.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/W_QOfA4kjq/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.23/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.23/test/contrast1.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/W_QOfA4kjq/contrast.vcf.gz -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/W_QOfA4kjq/contrast.bcf -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/W_QOfA4kjq/contrast.1.vcf.gz -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/W_QOfA4kjq/contrast.1.bcf -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/W_QOfA4kjq/contrast.1.vcf.gz -a NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/W_QOfA4kjq/contrast.1.bcf -a NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.1.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.1.bcf -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.2.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.2.bcf -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.4.bcf -p proband,father,mother | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.8.vcf.gz -p proband,father,mother | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.8.bcf -p proband,father,mother | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.9.vcf.gz -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.9.bcf -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.9.vcf.gz -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.9.bcf -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.10.vcf.gz -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.10.bcf -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.11.vcf.gz -p 1X:proband,father,mother | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM:%POS DNM=[%DNM ]\tAD=[%AD ]\tQS=[%QS ]\tVAF=[%VAF ]\tVA=[%VA ]' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.11.bcf -p 1X:proband,father,mother | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM:%POS DNM=[%DNM ]\tAD=[%AD ]\tQS=[%QS ]\tVAF=[%VAF ]\tVA=[%VA ]' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.11.vcf.gz -p 1X:proband,father,mother --strictly-novel | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM:%POS DNM=[%DNM ]\tAD=[%AD ]\tQS=[%QS ]\tVAF=[%VAF ]\tVA=[%VA ]' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/W_QOfA4kjq/trio-dnm/trio-dnm.11.bcf -p 1X:proband,father,mother --strictly-novel | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM:%POS DNM=[%DNM ]\tAD=[%AD ]\tQS=[%QS ]\tVAF=[%VAF ]\tVA=[%VA ]' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +gvcfz /tmp/W_QOfA4kjq/gvcfz.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.23/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +gvcfz /tmp/W_QOfA4kjq/gvcfz.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.23/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +gvcfz /tmp/W_QOfA4kjq/gvcfz.vcf.gz -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.23/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +gvcfz /tmp/W_QOfA4kjq/gvcfz.bcf -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.23/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +gvcfz /tmp/W_QOfA4kjq/gvcfz.2.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +gvcfz /tmp/W_QOfA4kjq/gvcfz.2.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.1.vcf.gz -m overlap | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.1.bcf -m overlap | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.1.vcf.gz -m overlap -M overlap | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.1.bcf -m overlap -M overlap | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.1.vcf.gz -m overlap -O t | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.1.bcf -m overlap -O t | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.1.vcf.gz -m overlap --reverse | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.1.bcf -m overlap --reverse | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.1.vcf.gz -m dup -M DUP | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.1.bcf -m dup -M DUP | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.1.vcf.gz -m dup -M unique --reverse | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.1.bcf -m dup -M unique --reverse | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.2.vcf.gz -m 'min(QUAL)' -M rmme | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.2.bcf -m 'min(QUAL)' -M rmme | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.3.vcf.gz -m 'min(QUAL)' -M rmme | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.3.bcf -m 'min(QUAL)' -M rmme | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.3.vcf.gz -m 'min(QUAL)' -M rmme --missing 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.3.bcf -m 'min(QUAL)' -M rmme --missing 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.3.vcf.gz -m 'min(QUAL)' -M rmme --missing DP | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/W_QOfA4kjq/remove-overlaps.3.bcf -m 'min(QUAL)' -M rmme --missing DP | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -c Consequence -s worst:missense+:worst | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -c Consequence -s worst:missense+:worst | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -c Consequence -s worst:missense+:worst | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -c Consequence -s worst:missense+:worst | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -s worst:missense+:worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -s worst:missense+:worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -s CANONICAL=YES:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -s CANONICAL=YES:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -s primary:missense+:worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -s primary:missense+:worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -s CANONICAL=YES:missense+:worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -s CANONICAL=YES:missense+:worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -s CANONICAL=YES:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -s CANONICAL=YES:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.2.vcf.gz -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.2.bcf -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.2.vcf.gz -s worst -f'%POS\t%AF\n' -a BCSQ | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.2.bcf -s worst -f'%POS\t%AF\n' -a BCSQ | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.2.vcf.gz -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.2.bcf -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.2.vcf.gz -s worst -f'%POS\t%INFO/AF\n' -a BCSQ | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.2.bcf -s worst -f'%POS\t%INFO/AF\n' -a BCSQ | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.3.vcf.gz -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.3.bcf -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.3.vcf.gz -s worst::worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.3.bcf -s worst::worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d -H | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d -H | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d -HH | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d -HH | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A @@@ -d -H | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A @@@ -d -H | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.4.bcf -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n' -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.4.bcf -f '%POS\t%BCSQ\n' -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d -s ::worst | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.4.bcf -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d -s ::worst | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n' -A tab -d -s ::worst | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.4.bcf -f '%POS\t%BCSQ\n' -A tab -d -s ::worst | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.5.vcf.gz -s :synonymous -c Consequence | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.5.bcf -s :synonymous -c Consequence | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.5.vcf.gz -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.5.bcf -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.6.vcf.gz -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.6.bcf -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.6.vcf.gz -c - | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.6.bcf -c - | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.6.vcf.gz -c - -s worst | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.6.bcf -c - -s worst | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.7.vcf.gz --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.7.bcf --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.8.vcf.gz -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.8.bcf -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.8.vcf.gz -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.8.bcf -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.8.vcf.gz -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.8.bcf -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.9.vcf.gz -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.9.bcf -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.10.vcf.gz -a CSQ -f '%M_CAP_pred %M_CAP_score\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.10.bcf -a CSQ -f '%M_CAP_pred %M_CAP_score\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/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: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.10.vcf.gz -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.10.bcf -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' -g /builddir/build/BUILD/bcftools-1.23/test/split-vep.gene-list.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' -g /builddir/build/BUILD/bcftools-1.23/test/split-vep.gene-list.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' -g /builddir/build/BUILD/bcftools-1.23/test/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' -g /builddir/build/BUILD/bcftools-1.23/test/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' -g +/builddir/build/BUILD/bcftools-1.23/test/split-vep.gene-list.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' -g +/builddir/build/BUILD/bcftools-1.23/test/split-vep.gene-list.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' -g +/builddir/build/BUILD/bcftools-1.23/test/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' -g +/builddir/build/BUILD/bcftools-1.23/test/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.broken-LoF.vcf.gz -d -f '%CHROM:%POS %Consequence %LoF_info\n' -a vep | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.broken-LoF.bcf -d -f '%CHROM:%POS %Consequence %LoF_info\n' -a vep | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.broken-LoF.vcf.gz -d -f '%CHROM:%POS %LoF_info\n' -a vep -i 'Consequence=="frameshift_variant"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.broken-LoF.bcf -d -f '%CHROM:%POS %LoF_info\n' -a vep -i 'Consequence=="frameshift_variant"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -f'%POS\n' -i'SYMBOL~"SAMD11"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -f'%POS\n' -i'SYMBOL~"SAMD11"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.vcf.gz -f'%POS\t%MAX_AF\n' -i'MAX_AF>0.999' -c MAX_AF,MAX_AF:float,MAX_AF | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.bcf -f'%POS\t%MAX_AF\n' -i'MAX_AF>0.999' -c MAX_AF,MAX_AF:float,MAX_AF | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.filter.vcf.gz -s worst -i'CSQ~"nonsense"' -f '%POS %Consequence %Feature %BIOTYPE' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.filter.bcf -s worst -i'CSQ~"nonsense"' -f '%POS %Consequence %Feature %BIOTYPE' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.filter.vcf.gz -s worst -i'CSQ~"nonsense"' -f '%POS %Consequence %Feature %BIOTYPE %CSQ' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.filter.bcf -s worst -i'CSQ~"nonsense"' -f '%POS %Consequence %Feature %BIOTYPE %CSQ' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s primary | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s primary | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL=YES | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL=YES | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL!=YES | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL!=YES | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL= | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL= | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s mane | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s mane | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s MANE_SELECT!='' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s MANE_SELECT!='' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.vcf.gz -s mane | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.bcf -s mane | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.vcf.gz -s primary | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.bcf -s primary | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.vcf.gz -s PolyPhen~damaging | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.select-tr-expr.bcf -s PolyPhen~damaging | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.types.vcf.gz -f'%cDNA_position %CDS_position %Protein_position' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.types.bcf -f'%cDNA_position %CDS_position %Protein_position' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.types.vcf.gz -f'%cDNA_position %CDS_position %Protein_position' -c cDNA_position:int,CDS_position:int,Protein_position:int | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.types.bcf -f'%cDNA_position %CDS_position %Protein_position' -c cDNA_position:int,CDS_position:int,Protein_position:int | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.filter-missing-bt2098.vcf.gz -e 'gnomad_genomes_AF >= 0.02' | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %gnomad_genomes_AF ' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.filter-missing-bt2098.bcf -e 'gnomad_genomes_AF >= 0.02' | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %gnomad_genomes_AF ' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.filter-missing-bt2098.vcf.gz -i 'gnomad_genomes_AF < 0.02 || gnomad_genomes_AF=="."' | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %gnomad_genomes_AF ' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/W_QOfA4kjq/split-vep.filter-missing-bt2098.bcf -i 'gnomad_genomes_AF < 0.02 || gnomad_genomes_AF=="."' | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %gnomad_genomes_AF ' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/W_QOfA4kjq/parental-origin.vcf.gz -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/W_QOfA4kjq/parental-origin.bcf -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/W_QOfA4kjq/parental-origin.vcf.gz -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/W_QOfA4kjq/parental-origin.bcf -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/W_QOfA4kjq/parental-origin.vcf.gz -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/W_QOfA4kjq/parental-origin.bcf -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/W_QOfA4kjq/parental-origin.vcf.gz -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/W_QOfA4kjq/parental-origin.bcf -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/W_QOfA4kjq/parental-origin.vcf.gz -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/W_QOfA4kjq/parental-origin.bcf -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 1 -a r2,LD,HD /tmp/W_QOfA4kjq/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 1 -a r2,LD,HD /tmp/W_QOfA4kjq/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 1 -a r2,LD,HD /tmp/W_QOfA4kjq/prune.2.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 1 -a r2,LD,HD /tmp/W_QOfA4kjq/prune.2.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/W_QOfA4kjq/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/W_QOfA4kjq/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/W_QOfA4kjq/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/W_QOfA4kjq/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/W_QOfA4kjq/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/W_QOfA4kjq/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/W_QOfA4kjq/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/W_QOfA4kjq/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 -N 1st /tmp/W_QOfA4kjq/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 -N 1st /tmp/W_QOfA4kjq/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/W_QOfA4kjq/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/W_QOfA4kjq/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 3bp -a count -i 'XX!=0' -k /tmp/W_QOfA4kjq/prune.3.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 3bp -a count -i 'XX!=0' -k /tmp/W_QOfA4kjq/prune.3.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 3bp -a count -i 'XX!=0' /tmp/W_QOfA4kjq/prune.3.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 3bp -a count -i 'XX!=0' /tmp/W_QOfA4kjq/prune.3.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 3bp -m count=2 -i 'XX!=0' /tmp/W_QOfA4kjq/prune.3.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 3bp -m count=2 -i 'XX!=0' /tmp/W_QOfA4kjq/prune.3.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance /tmp/W_QOfA4kjq/variant-distance.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance /tmp/W_QOfA4kjq/variant-distance.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d nearest /tmp/W_QOfA4kjq/variant-distance.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d nearest /tmp/W_QOfA4kjq/variant-distance.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d fwd /tmp/W_QOfA4kjq/variant-distance.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d fwd /tmp/W_QOfA4kjq/variant-distance.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d rev /tmp/W_QOfA4kjq/variant-distance.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d rev /tmp/W_QOfA4kjq/variant-distance.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d both /tmp/W_QOfA4kjq/variant-distance.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d both /tmp/W_QOfA4kjq/variant-distance.bcf | grep -v ^##bcftools_ .. ok test_plugin_vrfs: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +vrfs -a /tmp/W_QOfA4kjq/mpileup.bam.list -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -s /builddir/build/BUILD/bcftools-1.23/test/vrfs.sites.txt | sort .. ok test_plugin_split: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/W_QOfA4kjq/split.1.1 && cd /tmp/W_QOfA4kjq/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-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done .. ok test_plugin_split: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/W_QOfA4kjq/split.1.2 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.2.txt && cd /tmp/W_QOfA4kjq/split.1.2 && for f in A.vcf B.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done .. ok test_plugin_split: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/W_QOfA4kjq/split.1.3 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.3.txt && cd /tmp/W_QOfA4kjq/split.1.3 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done .. ok test_plugin_split: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/W_QOfA4kjq/split.1.4 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.3.txt -i 'GT[0]="alt"' && cd /tmp/W_QOfA4kjq/split.1.4 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done .. ok test_plugin_split: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/W_QOfA4kjq/split.1.5 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.3.txt -i 'GT="alt"' && cd /tmp/W_QOfA4kjq/split.1.5 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done .. ok test_plugin_split: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/W_QOfA4kjq/split.1.6 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.4.txt -i 'GT="alt"' && cd /tmp/W_QOfA4kjq/split.1.6 && for f in file1.vcf file2.vcf file3.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done .. ok test_plugin_split: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/W_QOfA4kjq/split.1.7 -G /builddir/build/BUILD/bcftools-1.23/test/split.grp.1.1.txt && cd /tmp/W_QOfA4kjq/split.1.7 && for f in A.vcf A1.vcf A2.vcf B.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done .. ok test_plugin_split: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.2.vcf -o /tmp/W_QOfA4kjq/split.2.1 && cd /tmp/W_QOfA4kjq/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-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done .. ok test_plugin_scatter: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +scatter /builddir/build/BUILD/bcftools-1.23/test/scatter.1.vcf -o /tmp/W_QOfA4kjq/scatter.1.1 -n 3 && cd /tmp/W_QOfA4kjq/scatter.1.1 && cat 0.vcf 1.vcf 2.vcf | grep -v ^## .. ok test_plugin_scatter: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +scatter /builddir/build/BUILD/bcftools-1.23/test/scatter.1.vcf -o /tmp/W_QOfA4kjq/scatter.1.2 -s 21,22 && cd /tmp/W_QOfA4kjq/scatter.1.2 && cat 21.vcf 22.vcf | grep -v ^## .. ok test_plugin_scatter: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +scatter /builddir/build/BUILD/bcftools-1.23/test/scatter.1.vcf -o /tmp/W_QOfA4kjq/scatter.1.3 -s 21,22 -x X && cd /tmp/W_QOfA4kjq/scatter.1.3 && cat 21.vcf 22.vcf X.vcf | grep -v ^## .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -G /tmp/W_QOfA4kjq/concat.1.a.vcf.gz /tmp/W_QOfA4kjq/concat.1.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -G /tmp/W_QOfA4kjq/concat.1.a.vcf.gz /tmp/W_QOfA4kjq/concat.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -G /builddir/build/BUILD/bcftools-1.23/test/concat.1.a.vcf /builddir/build/BUILD/bcftools-1.23/test/concat.1.b.vcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version /tmp/W_QOfA4kjq/concat.1.a.vcf.gz /tmp/W_QOfA4kjq/concat.1.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob /tmp/W_QOfA4kjq/concat.1.a.vcf.gz /tmp/W_QOfA4kjq/concat.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version /builddir/build/BUILD/bcftools-1.23/test/concat.1.a.vcf /builddir/build/BUILD/bcftools-1.23/test/concat.1.b.vcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version /tmp/W_QOfA4kjq/concat.1.a.bcf /tmp/W_QOfA4kjq/concat.1.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob /tmp/W_QOfA4kjq/concat.1.a.bcf /tmp/W_QOfA4kjq/concat.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -a /tmp/W_QOfA4kjq/concat.2.a.vcf.gz /tmp/W_QOfA4kjq/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -a /tmp/W_QOfA4kjq/concat.2.a.vcf.gz /tmp/W_QOfA4kjq/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -a /tmp/W_QOfA4kjq/concat.2.a.bcf /tmp/W_QOfA4kjq/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -a /tmp/W_QOfA4kjq/concat.2.a.bcf /tmp/W_QOfA4kjq/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -aD /tmp/W_QOfA4kjq/concat.2.a.vcf.gz /tmp/W_QOfA4kjq/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -aD /tmp/W_QOfA4kjq/concat.2.a.vcf.gz /tmp/W_QOfA4kjq/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -aD /tmp/W_QOfA4kjq/concat.2.a.bcf /tmp/W_QOfA4kjq/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -aD /tmp/W_QOfA4kjq/concat.2.a.bcf /tmp/W_QOfA4kjq/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l --ligate-warn /tmp/W_QOfA4kjq/concat.3.a.vcf.gz /tmp/W_QOfA4kjq/concat.3.b.vcf.gz /tmp/W_QOfA4kjq/concat.3.0.vcf.gz /tmp/W_QOfA4kjq/concat.3.c.vcf.gz /tmp/W_QOfA4kjq/concat.3.d.vcf.gz /tmp/W_QOfA4kjq/concat.3.e.vcf.gz /tmp/W_QOfA4kjq/concat.3.f.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-warn /tmp/W_QOfA4kjq/concat.3.a.vcf.gz /tmp/W_QOfA4kjq/concat.3.b.vcf.gz /tmp/W_QOfA4kjq/concat.3.0.vcf.gz /tmp/W_QOfA4kjq/concat.3.c.vcf.gz /tmp/W_QOfA4kjq/concat.3.d.vcf.gz /tmp/W_QOfA4kjq/concat.3.e.vcf.gz /tmp/W_QOfA4kjq/concat.3.f.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l --ligate-warn /tmp/W_QOfA4kjq/concat.3.a.bcf /tmp/W_QOfA4kjq/concat.3.b.bcf /tmp/W_QOfA4kjq/concat.3.0.bcf /tmp/W_QOfA4kjq/concat.3.c.bcf /tmp/W_QOfA4kjq/concat.3.d.bcf /tmp/W_QOfA4kjq/concat.3.e.bcf /tmp/W_QOfA4kjq/concat.3.f.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-warn /tmp/W_QOfA4kjq/concat.3.a.bcf /tmp/W_QOfA4kjq/concat.3.b.bcf /tmp/W_QOfA4kjq/concat.3.0.bcf /tmp/W_QOfA4kjq/concat.3.c.bcf /tmp/W_QOfA4kjq/concat.3.d.bcf /tmp/W_QOfA4kjq/concat.3.e.bcf /tmp/W_QOfA4kjq/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 790029617 .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --naive-force /tmp/W_QOfA4kjq/naive_concat.0.bcf /tmp/W_QOfA4kjq/naive_concat.1.bcf /tmp/W_QOfA4kjq/naive_concat.2.bcf /tmp/W_QOfA4kjq/naive_concat.3.bcf /tmp/W_QOfA4kjq/naive_concat.4.bcf /tmp/W_QOfA4kjq/naive_concat.5.bcf /tmp/W_QOfA4kjq/naive_concat.6.bcf /tmp/W_QOfA4kjq/naive_concat.7.bcf /tmp/W_QOfA4kjq/naive_concat.8.bcf /tmp/W_QOfA4kjq/naive_concat.9.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view -H .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --naive /tmp/W_QOfA4kjq/naive_concat.0.vcf.gz /tmp/W_QOfA4kjq/naive_concat.1.vcf.gz /tmp/W_QOfA4kjq/naive_concat.2.vcf.gz /tmp/W_QOfA4kjq/naive_concat.3.vcf.gz /tmp/W_QOfA4kjq/naive_concat.4.vcf.gz /tmp/W_QOfA4kjq/naive_concat.5.vcf.gz /tmp/W_QOfA4kjq/naive_concat.6.vcf.gz /tmp/W_QOfA4kjq/naive_concat.7.vcf.gz /tmp/W_QOfA4kjq/naive_concat.8.vcf.gz /tmp/W_QOfA4kjq/naive_concat.9.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view -H .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l /tmp/W_QOfA4kjq/concat.4.a.vcf.gz /tmp/W_QOfA4kjq/concat.4.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l /tmp/W_QOfA4kjq/concat.4.a.vcf.gz /tmp/W_QOfA4kjq/concat.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l /tmp/W_QOfA4kjq/concat.4.a.bcf /tmp/W_QOfA4kjq/concat.4.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l /tmp/W_QOfA4kjq/concat.4.a.bcf /tmp/W_QOfA4kjq/concat.4.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l --ligate-warn /tmp/W_QOfA4kjq/concat.5.a.vcf.gz /tmp/W_QOfA4kjq/concat.5.b.vcf.gz /tmp/W_QOfA4kjq/concat.5.c.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-warn /tmp/W_QOfA4kjq/concat.5.a.vcf.gz /tmp/W_QOfA4kjq/concat.5.b.vcf.gz /tmp/W_QOfA4kjq/concat.5.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l --ligate-warn /tmp/W_QOfA4kjq/concat.5.a.bcf /tmp/W_QOfA4kjq/concat.5.b.bcf /tmp/W_QOfA4kjq/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-warn /tmp/W_QOfA4kjq/concat.5.a.bcf /tmp/W_QOfA4kjq/concat.5.b.bcf /tmp/W_QOfA4kjq/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l --ligate-force /tmp/W_QOfA4kjq/concat.5.a.bcf /tmp/W_QOfA4kjq/concat.5.b.bcf /tmp/W_QOfA4kjq/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-force /tmp/W_QOfA4kjq/concat.5.a.bcf /tmp/W_QOfA4kjq/concat.5.b.bcf /tmp/W_QOfA4kjq/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -G -a -D /tmp/W_QOfA4kjq/concat.5.a.vcf.gz /tmp/W_QOfA4kjq/concat.5.b.vcf.gz /tmp/W_QOfA4kjq/concat.5.c.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -G -a -D /tmp/W_QOfA4kjq/concat.5.a.vcf.gz /tmp/W_QOfA4kjq/concat.5.b.vcf.gz /tmp/W_QOfA4kjq/concat.5.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -G -a -D /tmp/W_QOfA4kjq/concat.5.a.bcf /tmp/W_QOfA4kjq/concat.5.b.bcf /tmp/W_QOfA4kjq/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -G -a -D /tmp/W_QOfA4kjq/concat.5.a.bcf /tmp/W_QOfA4kjq/concat.5.b.bcf /tmp/W_QOfA4kjq/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.hdr /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.hdr /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.hdr /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -N /builddir/build/BUILD/bcftools-1.23/test/reheader.samples /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -N /builddir/build/BUILD/bcftools-1.23/test/reheader.samples | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -N /builddir/build/BUILD/bcftools-1.23/test/reheader.samples /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -N /builddir/build/BUILD/bcftools-1.23/test/reheader.samples | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -N /builddir/build/BUILD/bcftools-1.23/test/reheader.samples /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -N /builddir/build/BUILD/bcftools-1.23/test/reheader.samples | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -n AAA,BBB /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -n AAA,BBB | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -n AAA,BBB /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -n AAA,BBB | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -n AAA,BBB /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -n AAA,BBB | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples2 /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples2 /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples2 /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples3 /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples3 /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples3 /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples4 /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples4 /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples4 /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.empty.hdr /builddir/build/BUILD/bcftools-1.23/test/empty.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.23/test/empty.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.empty.hdr /tmp/W_QOfA4kjq/empty.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/empty.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.empty.hdr /tmp/W_QOfA4kjq/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W_QOfA4kjq/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -f /builddir/build/BUILD/bcftools-1.23/test/reheader.fai /builddir/build/BUILD/bcftools-1.23/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -f /builddir/build/BUILD/bcftools-1.23/test/reheader.fai /tmp/W_QOfA4kjq/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -f /builddir/build/BUILD/bcftools-1.23/test/reheader.fai /tmp/W_QOfA4kjq/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.23/test/reheader.fai /builddir/build/BUILD/bcftools-1.23/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.23/test/reheader.fai /tmp/W_QOfA4kjq/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.23/test/reheader.fai /tmp/W_QOfA4kjq/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -f /builddir/build/BUILD/bcftools-1.23/test/reheader.3.fai /builddir/build/BUILD/bcftools-1.23/test/reheader.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -f /builddir/build/BUILD/bcftools-1.23/test/reheader.3.fai /tmp/W_QOfA4kjq/reheader.3.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.23/bcftools reheader -f /builddir/build/BUILD/bcftools-1.23/test/reheader.3.fai /tmp/W_QOfA4kjq/reheader.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.23/bcftools annotate --rename-chrs /tmp/W_QOfA4kjq/rename.map -Ov /tmp/W_QOfA4kjq/annotate.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.23/bcftools annotate --rename-chrs /tmp/W_QOfA4kjq/rename.map -Ob /tmp/W_QOfA4kjq/annotate.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.23/bcftools annotate --rename-chrs /tmp/W_QOfA4kjq/rename.map -Ov /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.23/bcftools annotate --rename-chrs /tmp/W_QOfA4kjq/rename.map -Ob /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. /tmp/W_QOfA4kjq/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --vcf-ids /tmp/W_QOfA4kjq/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --vcf-ids --3N6 /tmp/W_QOfA4kjq/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- /tmp/W_QOfA4kjq/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^## .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --tag PL /tmp/W_QOfA4kjq/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --tag PL /tmp/W_QOfA4kjq/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --vcf-ids /tmp/W_QOfA4kjq/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --vcf-ids /tmp/W_QOfA4kjq/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --3N6 /tmp/W_QOfA4kjq/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --3N6 /tmp/W_QOfA4kjq/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --3N6 --vcf-ids /tmp/W_QOfA4kjq/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --3N6 --vcf-ids /tmp/W_QOfA4kjq/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -h -,.,. /tmp/W_QOfA4kjq/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -h -,.,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -h .,-,. /tmp/W_QOfA4kjq/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -h .,-,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -h .,-,. --vcf-ids /tmp/W_QOfA4kjq/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert -h .,.,- /tmp/W_QOfA4kjq/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert -H /builddir/build/BUILD/bcftools-1.23/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.23/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.23/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert -H /builddir/build/BUILD/bcftools-1.23/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.23/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.23/test/convert.hls.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^## .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert --haplegendsample -,.,. /tmp/W_QOfA4kjq/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.hap-missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample -,. /tmp/W_QOfA4kjq/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample -,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample -,. --vcf-ids /tmp/W_QOfA4kjq/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample .,- /tmp/W_QOfA4kjq/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/W_QOfA4kjq/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/W_QOfA4kjq/convert.gvcf.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/W_QOfA4kjq/convert.gvcf.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.23/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.23/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.23andme | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert --no-version -c -,CHROM,POS,REF,ALT -f /builddir/build/BUILD/bcftools-1.23/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.tsv .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.23/bcftools convert -Ou -c -,CHROM,POS,REF,ALT -f /builddir/build/BUILD/bcftools-1.23/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.tsv | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.gvcf-missing.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.gvcf-missing.fa --missing N .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.gvcf-missing.1.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.gvcf-missing.fa --missing N .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.overlaps.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.2.fa -s A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.overlaps.1.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.2.fa -s A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.overlaps.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.overlaps.1.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.overlaps.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.overlaps.1.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.overlaps.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.overlaps.1.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.overlaps.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.overlaps.1.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.beyond.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.beyond.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.beyond.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.beyond.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab -c /tmp/W_QOfA4kjq/consensus.1.chain.new >/dev/null; cat /tmp/W_QOfA4kjq/consensus.1.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab -c /tmp/W_QOfA4kjq/consensus.2.chain.new >/dev/null; cat /tmp/W_QOfA4kjq/consensus.2.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -I -s - -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -I -s - -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -I -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab --mask-with X -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab --mask-with lc .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -I -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab --mask-with X -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab -c /tmp/W_QOfA4kjq/consensus.3.chain.new >/dev/null; cat /tmp/W_QOfA4kjq/consensus.3.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H 1 -c /tmp/W_QOfA4kjq/consensus.4.chain.new >/dev/null; cat /tmp/W_QOfA4kjq/consensus.4.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus2.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus2.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/empty.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/empty.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus3.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus3.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus4.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus4.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus5.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus5.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus6.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus6.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus6.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus6.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus7.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus8.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus8.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus8.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus8.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus8.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus8.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.9.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.9.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.10.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.10.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.11.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.11.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.12.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.12.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.12.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.13.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.13.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.13.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.13.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.14.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.14.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.14.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.14.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.12.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.12.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.15.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.15.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -I .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.16.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -I .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H I .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.16.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H I .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.17.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -s - -M N -m /builddir/build/BUILD/bcftools-1.23/test/consensus.17.bed .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.17.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -s - -M N -m /builddir/build/BUILD/bcftools-1.23/test/consensus.17.bed .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.18.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.18.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.18.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.18.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.19.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.19.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.19.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.19.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.20.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -s - .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.20.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.20.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.20.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -S /builddir/build/BUILD/bcftools-1.23/test/consensus.20.b.txt .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.20.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -S /builddir/build/BUILD/bcftools-1.23/test/consensus.20.b.txt .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -S /builddir/build/BUILD/bcftools-1.23/test/consensus.20.a.txt .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.20.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -S /builddir/build/BUILD/bcftools-1.23/test/consensus.20.a.txt .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.21.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.21.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.21.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.21.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.22.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.22.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.22.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.22.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.22.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/W_QOfA4kjq/consensus.22.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 2 .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r 11:10-20 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/iupac.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/iupac.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r 11:10-20 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/iupac.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/iupac.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -b /tmp/W_QOfA4kjq/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob -b /tmp/W_QOfA4kjq/mpileup.bam.urllist | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -b /tmp/W_QOfA4kjq/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob -b /tmp/W_QOfA4kjq/mpileup.cram.urllist | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -b /tmp/W_QOfA4kjq/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob -b /tmp/W_QOfA4kjq/mpileup.bam.urllist | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -b /tmp/W_QOfA4kjq/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob -b /tmp/W_QOfA4kjq/mpileup.cram.urllist | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -G /builddir/build/BUILD/bcftools-1.23/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -G /builddir/build/BUILD/bcftools-1.23/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -G /builddir/build/BUILD/bcftools-1.23/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -G /builddir/build/BUILD/bcftools-1.23/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -G /builddir/build/BUILD/bcftools-1.23/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -G /builddir/build/BUILD/bcftools-1.23/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.1.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.2.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.3.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.3.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.3.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.3.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.3.2.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq.gff3 /builddir/build/BUILD/bcftools-1.23/test/csq.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq.chr.gff3 --unify-chr-names -,chr,- /builddir/build/BUILD/bcftools-1.23/test/csq.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq.2.gff /builddir/build/BUILD/bcftools-1.23/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq.2.gff --ncsq 64 /builddir/build/BUILD/bcftools-1.23/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.fa --unify-chr-names -,-,- /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.fa --unify-chr-names -,-,chr /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.fa --unify-chr-names -,chr,- /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.fa --unify-chr-names -,chr,chr /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.fa --unify-chr-names chr,chr,chr /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.fa --unify-chr-names chr,-,chr /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.fa --unify-chr-names chr,chr,- /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.fa --unify-chr-names chr,-,- /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.gff --unify-chr-names Chromosome,chr,- /builddir/build/BUILD/bcftools-1.23/test/csq.yychr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000593942/ENST00000593942.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000593942/ENST00000593942.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000593942/last-codon-deletion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000528237/ENST00000528237.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000528237/ENST00000528237.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/test/csq/ENST00000422159 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000390520/ENST00000390520.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000390520/ENST00000390520.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000390520/deletion-overlap.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/test/csq/ENST00000379416 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000301246/ENST00000301246.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000301246/ENST00000301246.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000301246/15bp-insert.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000571540/ENST00000571540.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000571540/ENST00000571540.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000571540/nmd.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000285021/ENST00000285021.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000285021/ENST00000285021.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000357367/ENST00000357367.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000357367/ENST00000357367.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000357367/stop-retained.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000230048/ENST00000230048.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000230048/ENST00000230048.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000230048/start-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/test/csq/ENST00000368801.2 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000368801.2.fa -g ENST00000368801.2.gff alt-gencode.vcf -v 0 -C 0 | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%BCSQ\n' | ../sort-csq -q .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801.2 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000368801.2.fa -g ENST00000368801.2.gff alt-gencode.vcf -v 0 -C 1 | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%BCSQ\n' | ../sort-csq -q .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801.2/ENST00000368801.2.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801.2/start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000518414/ENST00000518414.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000518414/ENST00000518414.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000382647/ENST00000382647.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000382647/ENST00000382647.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/test/csq/ENST00000000001 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000000001.fa -g ENST00000000001.gff test.vcf -p a -Ot | grep -v ^# .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000000001 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000000001.fa -g ENST00000000001.gff test.vcf -p a | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000400151/ENST00000400151.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000400151/ENST00000400151.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000400151/long-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/test/csq/ENST00000580206 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000519442/ENST00000519442.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000519442/ENST00000519442.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000519442/synon-splice-region-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420190/ENST00000420190.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420190/ENST00000420190.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420190/abort-in-csq-push.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000557788/ENST00000557788.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000557788/ENST00000557788.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000557788/long-overlap-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0003/EDUMMY0003.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0003/EDUMMY0003.gff /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0003/long-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/test/csq/ENSMUST00000133836 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000436063/ENST00000436063.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000436063/ENST00000436063.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000436063/insert-before-utr.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000375992/ENST00000375992.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000375992/ENST00000375992.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249.2/ENST00000318249.2.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0002/EDUMMY0002.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0002/EDUMMY0002.gff /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0002/boundaries.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000269081/ENST00000269081.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000269081/ENST00000269081.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000271583/ENST00000271583.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000271583/ENST00000271583.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000271583/splice-acceptor.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000256452/ENST00000256452.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000256452/ENST00000256452.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000256452/intron.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENSCAFT00000047742/ENSCAFT00000047742.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENSCAFT00000047742/ENSCAFT00000047742.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENSCAFT00000047742/test.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573035-bt2212/complex-event.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000227471/ENST00000227471.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000227471/ENST00000227471.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000624631/ENST00000624631.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000624631/ENST00000624631.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000624631/ambiguous.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000410009/ENST00000410009.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000410009/ENST00000410009.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000410009/frameshift.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000360372/ENST00000360372.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000360372/ENST00000360372.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000360372/mnp.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000409523/ENST00000409523.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000409523/ENST00000409523.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000409523/long-overlapping-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/start-lost-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000545279/ENST00000545279.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000545279/ENST00000545279.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000545279/splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420670/start-stop-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420670/segfault.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000381157/ENST00000381157.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000381157/ENST00000381157.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000381157/haploid-diploid.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520868/ENST00000520868.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520868/ENST00000520868.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520868/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801/ENST00000368801.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801/ENST00000368801.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801/compound-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000448695/ENST00000448695.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000448695/ENST00000448695.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENSG00000173376/ENSG00000173376.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENSG00000173376/ENSG00000173376.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENSG00000173376/synon.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000413103/ENST00000413103.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000413103/ENST00000413103.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000413103/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/test/csq/ENST00000000000 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000263103-INS/insertions.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.23/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.23/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/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-1.23/bcftools gtcheck --keep-refs /tmp/W_QOfA4kjq/gtcheck.gvcf.a.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.gvcf.b.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck --keep-refs /tmp/W_QOfA4kjq/gtcheck.gvcf.b.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.gvcf.a.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck /tmp/W_QOfA4kjq/gtcheck.gvcf.a.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.gvcf.b.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck /tmp/W_QOfA4kjq/gtcheck.gvcf.b.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.gvcf.a.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 --no-HWE-prob /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u GT,GT /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u GT,PL /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u PL,GT /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u PL,PL /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -p s1,s1 /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 /tmp/W_QOfA4kjq/gtcheck.2.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 /tmp/W_QOfA4kjq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/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/W_QOfA4kjq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.23/test/gtcheck.3.pairs /tmp/W_QOfA4kjq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u PL /tmp/W_QOfA4kjq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 --n-matches 4 /tmp/W_QOfA4kjq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/W_QOfA4kjq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/W_QOfA4kjq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/W_QOfA4kjq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/W_QOfA4kjq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/W_QOfA4kjq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -p B,C,B,D /tmp/W_QOfA4kjq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u GT,GT -H /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u GT,PL -H /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u PL,GT -H /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u PL,PL -H /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.23/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/W_QOfA4kjq/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.23/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/W_QOfA4kjq/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -u GT -e 30 /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -u GT -e 300 /tmp/W_QOfA4kjq/gtcheck.1.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -u PL -e 30 /tmp/W_QOfA4kjq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck /tmp/W_QOfA4kjq/gtcheck.ntop.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck --n-matches 2 /tmp/W_QOfA4kjq/gtcheck.ntop.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck /tmp/W_QOfA4kjq/gtcheck.5.vcf.gz -g /tmp/W_QOfA4kjq/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -p A,B,B,C /tmp/W_QOfA4kjq/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/W_QOfA4kjq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +vcf2table /tmp/W_QOfA4kjq/merge.4.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +vcf2table /tmp/W_QOfA4kjq/merge.4.b.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +vcf2table /tmp/W_QOfA4kjq/split-vep.2.vcf.gz -- --hide 'INFO,URL' | grep -v ^##bcftools_ .. ok test_vcf_plugin: export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +vcf2table /tmp/W_QOfA4kjq/split-vep.2.bcf -- --hide 'INFO,URL' | grep -v ^##bcftools_ .. ok Number of tests: total .. 2396 passed .. 2396 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: bcftools-1.23-1.el9.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.P90EQp + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.23 + DOCDIR=/builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/share/doc/bcftools + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/share/doc/bcftools + cp -pr AUTHORS /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/share/doc/bcftools + cp -pr NEWS /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/share/doc/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.OdjFp5 + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.23 + LICENSEDIR=/builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/share/licenses/bcftools + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/share/licenses/bcftools + cp -pr LICENSE /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64/usr/share/licenses/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Provides: bcftools = 1.23-1.el9 bcftools(aarch-64) = 1.23-1.el9 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) libgsl.so.25()(64bit) libgslcblas.so.0()(64bit) libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(64bit) libhts.so.3(HTSLIB_1.1)(64bit) libhts.so.3(HTSLIB_1.10)(64bit) libhts.so.3(HTSLIB_1.13)(64bit) libhts.so.3(HTSLIB_1.16)(64bit) libhts.so.3(HTSLIB_1.17)(64bit) libhts.so.3(HTSLIB_1.2.1)(64bit) libhts.so.3(HTSLIB_1.22)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.6)(64bit) libhts.so.3(HTSLIB_1.7)(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.5.32()(64bit) rtld(GNU_HASH) Conflicts: samtools < 1.0 Processing files: bcftools-debugsource-1.23-1.el9.aarch64 Provides: bcftools-debugsource = 1.23-1.el9 bcftools-debugsource(aarch-64) = 1.23-1.el9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bcftools-debuginfo-1.23-1.el9.aarch64 Provides: bcftools-debuginfo = 1.23-1.el9 bcftools-debuginfo(aarch-64) = 1.23-1.el9 debuginfo(build-id) = 002dbf5a2ff53b1c66f3113909985d3848d7da01 debuginfo(build-id) = 01f50ef53059876856193b90bb70d44fafb075fd debuginfo(build-id) = 0502997774a581d95e615074249a162e6d592381 debuginfo(build-id) = 0fadf5a33b215327fe1225b4539cbc50040a2963 debuginfo(build-id) = 24d49a172aff4148268735443be33ea90ea5f4bd debuginfo(build-id) = 34d9df37e736e7d1c5c2ba09c5a986ffdf242490 debuginfo(build-id) = 387327a2cb54da80f5458493f7d796a902af181a debuginfo(build-id) = 392f43e9e0a06a07d3d03b7fe6cc4a917e7371fb debuginfo(build-id) = 3c9b178ad7744f74c86b6ef46b4cdf54923772bd debuginfo(build-id) = 3f74f4c78cf8501001869e75b39c0855ef55dc9a debuginfo(build-id) = 5ad14ca741674637a645cb0836f947c5b9eddef8 debuginfo(build-id) = 5af1b51c3adde6af89926e3368da479536596ad8 debuginfo(build-id) = 5bef944b361963bd6496b8fa08335afa46c3dc5c debuginfo(build-id) = 5c7bb0cb2f9d3794a7974e1c3d15575edda17f47 debuginfo(build-id) = 5f2504307a1579633235c2d76f05ede6ff8f2954 debuginfo(build-id) = 6cbac717c924e299b894392c3e575ea594022a09 debuginfo(build-id) = 780a86e0cde5dd2d3565532822935d84f30c09f2 debuginfo(build-id) = 7997bdb641a759c7a46f523ea37246c69e628f25 debuginfo(build-id) = 7d24c46d4fd66405ab421e2aab1dd2711c9370c1 debuginfo(build-id) = 8229cb69a636bc46ac09a8a9a1dc06416821e135 debuginfo(build-id) = 8c1dddf8f5804d9ec894437ae022697f848f1ebc debuginfo(build-id) = 8efd0bd21d71d3ea90806c9b7774624d6070dcc2 debuginfo(build-id) = 9572e08d212a8657e322cc4e24fe1b42553c75d2 debuginfo(build-id) = 96e6547f3510d185a4d493144b2cc7eeaee45954 debuginfo(build-id) = 971d4b568ae8301fad1cc836cd786580f776c2cf debuginfo(build-id) = 9855c720ff467163c639731329ddf09c6997b333 debuginfo(build-id) = 9be4d6adf826b9a9c33bf59a9d3929d63f8b30f8 debuginfo(build-id) = a8273cf74209928921cbeeac1b3e1aa9f7838d35 debuginfo(build-id) = ac892d5255dfa093e0a6cdc467f42cb7db67af76 debuginfo(build-id) = af00eed7129c7552fea366fd031306e4ea44cc6c debuginfo(build-id) = b1e1f8a2102ab970ce7fa543805fb82fc9a6e207 debuginfo(build-id) = b4a7fd5f4d8e4fa0702254adbbe8ea2b59db2f08 debuginfo(build-id) = bbe915189596e581f916cf3d88545e4b74fb6b0f debuginfo(build-id) = be0d75708188d822f4a0bedff6eecda41e0af701 debuginfo(build-id) = c0a774edb47716797e13668a65c4aa3e86f407ed debuginfo(build-id) = d015550c569f0b8bad861a9681cdc414ad701f64 debuginfo(build-id) = ddc71f8f080f4401d6025039c0ace5db4088c4ff debuginfo(build-id) = e6d31daf17f6d167896efff13d2293675ef0bfb6 debuginfo(build-id) = e7c8c4d23c38202341253209ed323b1d8d1c7488 debuginfo(build-id) = ea04bbebf1f40dfeda5a6fca1531d248cd9dc104 debuginfo(build-id) = ec73ac1f52028577e4dc6a25b3e141727282daba debuginfo(build-id) = ee612e92f2f8dfa941db0062347634861382200d Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bcftools-debugsource(aarch-64) = 1.23-1.el9 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64 Wrote: /builddir/build/RPMS/bcftools-1.23-1.el9.aarch64.rpm Wrote: /builddir/build/RPMS/bcftools-debugsource-1.23-1.el9.aarch64.rpm Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.23-1.el9.aarch64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.pRjxcU + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.23 + /usr/bin/rm -rf /builddir/build/BUILDROOT/bcftools-1.23-1.el9.aarch64 + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild bcftools-1.23-1.el9.src.rpm Finish: build phase for bcftools-1.23-1.el9.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-9-aarch64-1769508937.072208/root/var/log/dnf.rpm.log /var/lib/mock/rhel+epel-9-aarch64-1769508937.072208/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-9-aarch64-1769508937.072208/root/var/log/dnf.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-1.23-1.el9.src.rpm) Config(child) 1 minutes 47 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": "1.23", "release": "1.el9", "arch": "aarch64" }, { "name": "bcftools", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "aarch64" }, { "name": "bcftools", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "src" }, { "name": "bcftools-debuginfo", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "aarch64" } ] } RPMResults finished