https://launchpad.net/ubuntu/+source/bcftools/1.10.2-4/+build/19591624 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-079 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 15 Jul 05:13:15 ntpdate[1937]: adjust time server 10.211.37.1 offset 0.018851 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-19591624 --image-type chroot /home/buildd/filecache-default/bb4dbf4bd068f4f4da4a9ba56413a8aa8579df72 Creating target for build PACKAGEBUILD-19591624 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-19591624 Starting target for build PACKAGEBUILD-19591624 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-19591624 'deb http://ftpmaster.internal/ubuntu groovy main universe' 'deb http://ftpmaster.internal/ubuntu groovy-security main universe' 'deb http://ftpmaster.internal/ubuntu groovy-updates main universe' 'deb http://ftpmaster.internal/ubuntu groovy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-19591624 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-19591624 Updating target for build PACKAGEBUILD-19591624 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-security InRelease [89.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-updates InRelease [89.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main arm64 Packages [948 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe arm64 Packages [8584 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5204 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 Packages [68.2 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [39.3 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 Packages [752 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [332 kB] Fetched 17.0 MB in 6s (2795 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libhogweed5 libnettle7 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libhogweed6 libnettle8 The following packages will be upgraded: apt base-files bash binutils binutils-aarch64-linux-gnu binutils-common bsdutils build-essential bzip2 ca-certificates coreutils cpp-9 dash debconf debianutils diffutils dpkg dpkg-dev e2fsprogs fdisk g++-9 gcc-10-base gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan5 libassuan0 libatomic1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfdisk1 libgcc-9-dev libgcc-s1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libidn2-0 libitm1 libjson-c4 libkmod2 liblsan0 liblzma5 libmount1 libmpfr6 libncurses6 libncursesw6 libnpth0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre3 libperl5.30 libprocps8 libseccomp2 libselinux1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libtsan0 libubsan1 libudev1 libunistring2 libuuid1 libzstd1 linux-libc-dev login logsave make mount ncurses-base ncurses-bin openssl passwd perl perl-base perl-modules-5.30 pinentry-curses pkgbinarymangler procps sed systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata ubuntu-keyring util-linux xz-utils 125 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 63.7 MB of archives. After this operation, 1539 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy/main arm64 libcrypt-dev arm64 1:4.4.16-1ubuntu1 [111 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main arm64 libc6-dev arm64 2.31-0ubuntu10 [2059 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main arm64 libc-dev-bin arm64 2.31-0ubuntu10 [64.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main arm64 libcrypt1 arm64 1:4.4.16-1ubuntu1 [82.5 kB] Get:5 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 linux-libc-dev arm64 5.4.0-40.44 [1089 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main arm64 libatomic1 arm64 10.1.0-3ubuntu1 [9868 B] Get:7 http://ftpmaster.internal/ubuntu groovy/main arm64 libubsan1 arm64 10.1.0-3ubuntu1 [127 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main arm64 libtsan0 arm64 10.1.0-3ubuntu1 [302 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main arm64 liblsan0 arm64 10.1.0-3ubuntu1 [130 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main arm64 libitm1 arm64 10.1.0-3ubuntu1 [24.2 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main arm64 libgomp1 arm64 10.1.0-3ubuntu1 [93.2 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main arm64 gcc-10-base arm64 10.1.0-3ubuntu1 [20.1 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main arm64 libgcc-s1 arm64 10.1.0-3ubuntu1 [34.7 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main arm64 libcc1-0 arm64 10.1.0-3ubuntu1 [37.1 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main arm64 libstdc++6 arm64 10.1.0-3ubuntu1 [463 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main arm64 libc6 arm64 2.31-0ubuntu10 [2266 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main arm64 base-files arm64 11ubuntu9 [60.0 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main arm64 debianutils arm64 4.11 [85.3 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main arm64 bash arm64 5.0-6ubuntu2 [603 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main arm64 bsdutils arm64 1:2.35.2-7ubuntu3 [82.5 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main arm64 coreutils arm64 8.30-3ubuntu3 [1165 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main arm64 dpkg arm64 1.19.7ubuntu4 [1113 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main arm64 perl-modules-5.30 all 5.30.3-4 [2740 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main arm64 libperl5.30 arm64 5.30.3-4 [3748 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main arm64 perl arm64 5.30.3-4 [223 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main arm64 perl-base arm64 5.30.3-4 [1391 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main arm64 bzip2 arm64 1.0.8-3ubuntu1 [32.5 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main arm64 libbz2-1.0 arm64 1.0.8-3ubuntu1 [32.7 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main arm64 debconf all 1.5.74 [121 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main arm64 dash arm64 0.5.10.2-7 [84.2 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main arm64 diffutils arm64 1:3.7-3build1 [189 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main arm64 gzip arm64 1.10-2ubuntu1 [92.8 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main arm64 login arm64 1:4.8.1-1ubuntu6 [218 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main arm64 ncurses-bin arm64 6.2-1 [167 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main arm64 sed arm64 4.7-1build1 [185 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main arm64 libblkid1 arm64 2.35.2-7ubuntu3 [125 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main arm64 libuuid1 arm64 2.35.2-7ubuntu3 [21.3 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main arm64 libfdisk1 arm64 2.35.2-7ubuntu3 [157 kB] Get:39 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libselinux1 arm64 3.1-1 [65.2 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main arm64 libmount1 arm64 2.35.2-7ubuntu3 [137 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main arm64 libncurses6 arm64 6.2-1 [91.8 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main arm64 libncursesw6 arm64 6.2-1 [120 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main arm64 libtinfo6 arm64 6.2-1 [81.2 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main arm64 libsmartcols1 arm64 2.35.2-7ubuntu3 [89.3 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main arm64 fdisk arm64 2.35.2-7ubuntu3 [118 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main arm64 util-linux arm64 2.35.2-7ubuntu3 [1007 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main arm64 init-system-helpers all 1.58 [38.4 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main arm64 libc-bin arm64 2.31-0ubuntu10 [504 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main arm64 ncurses-base all 6.2-1 [18.7 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main arm64 sysvinit-utils arm64 2.96-3ubuntu1 [20.4 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main arm64 libgpg-error0 arm64 1.38-2 [59.8 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main arm64 libgcrypt20 arm64 1.8.5-5ubuntu2 [350 kB] Get:53 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 liblzma5 arm64 5.2.4-1ubuntu1 [87.9 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main arm64 systemd-sysv arm64 245.6-2ubuntu1 [10.3 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main arm64 systemd-timesyncd arm64 245.6-2ubuntu1 [26.2 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main arm64 libacl1 arm64 2.2.53-8 [17.9 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main arm64 libapparmor1 arm64 2.13.3-7ubuntu6 [33.1 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main arm64 libcap2 arm64 1:2.36-1 [16.1 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main arm64 libargon2-1 arm64 0~20171227-0.2build20.10.0 [18.5 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main arm64 libudev1 arm64 245.6-2ubuntu1 [68.6 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main arm64 libdevmapper1.02.1 arm64 2:1.02.167-1ubuntu3 [110 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main arm64 libjson-c4 arm64 0.13.1+dfsg-9 [28.3 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main arm64 libssl1.1 arm64 1.1.1f-1ubuntu3 [1154 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main arm64 libcryptsetup12 arm64 2:2.3.3-1ubuntu3 [176 kB] Get:65 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libnettle8 arm64 3.6-1build1 [130 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main arm64 libgmp10 arm64 2:6.2.0+dfsg-6 [217 kB] Get:67 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libhogweed6 arm64 3.6-1build1 [190 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main arm64 libunistring2 arm64 0.9.10-4 [359 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main arm64 libidn2-0 arm64 2.3.0-1 [51.9 kB] Get:70 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libgnutls30 arm64 3.6.13-4ubuntu4 [692 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main arm64 libkmod2 arm64 27+20200310-2ubuntu1 [40.7 kB] Get:72 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libpam0g arm64 1.3.1-5ubuntu5 [53.9 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main arm64 libseccomp2 arm64 2.4.3-1ubuntu4 [39.8 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main arm64 mount arm64 2.35.2-7ubuntu3 [115 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/main arm64 systemd arm64 245.6-2ubuntu1 [3492 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/main arm64 libsystemd0 arm64 245.6-2ubuntu1 [246 kB] Get:77 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libzstd1 arm64 1.4.5+dfsg-3 [277 kB] Get:78 http://ftpmaster.internal/ubuntu groovy/main arm64 libapt-pkg6.0 arm64 2.1.7 [769 kB] Get:79 http://ftpmaster.internal/ubuntu groovy/main arm64 gpgv arm64 2.2.20-1ubuntu1 [184 kB] Get:80 http://ftpmaster.internal/ubuntu groovy/main arm64 ubuntu-keyring all 2020.06.17.1 [22.2 kB] Get:81 http://ftpmaster.internal/ubuntu groovy/main arm64 apt arm64 2.1.7 [1238 kB] Get:82 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libpam-modules-bin arm64 1.3.1-5ubuntu5 [35.7 kB] Get:83 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libpam-modules arm64 1.3.1-5ubuntu5 [242 kB] Get:84 http://ftpmaster.internal/ubuntu groovy/main arm64 logsave arm64 1.45.6-1ubuntu1 [10.2 kB] Get:85 http://ftpmaster.internal/ubuntu groovy/main arm64 libext2fs2 arm64 1.45.6-1ubuntu1 [177 kB] Get:86 http://ftpmaster.internal/ubuntu groovy/main arm64 e2fsprogs arm64 1.45.6-1ubuntu1 [504 kB] Get:87 http://ftpmaster.internal/ubuntu groovy/main arm64 init arm64 1.58 [6172 B] Get:88 http://ftpmaster.internal/ubuntu groovy/main arm64 libcap-ng0 arm64 0.7.9-2.2 [10.6 kB] Get:89 http://ftpmaster.internal/ubuntu groovy/main arm64 libdebconfclient0 arm64 0.252ubuntu1 [6196 B] Get:90 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libpam-runtime all 1.3.1-5ubuntu5 [37.3 kB] Get:91 http://ftpmaster.internal/ubuntu groovy/main arm64 libpcre3 arm64 2:8.39-13 [209 kB] Get:92 http://ftpmaster.internal/ubuntu groovy/main arm64 libsepol1 arm64 3.1-1 [234 kB] Get:93 http://ftpmaster.internal/ubuntu groovy/main arm64 passwd arm64 1:4.8.1-1ubuntu6 [770 kB] Get:94 http://ftpmaster.internal/ubuntu groovy/main arm64 libcom-err2 arm64 1.45.6-1ubuntu1 [9336 B] Get:95 http://ftpmaster.internal/ubuntu groovy/main arm64 libprocps8 arm64 2:3.3.16-5ubuntu1 [31.5 kB] Get:96 http://ftpmaster.internal/ubuntu groovy/main arm64 libss2 arm64 1.45.6-1ubuntu1 [10.7 kB] Get:97 http://ftpmaster.internal/ubuntu groovy/main arm64 procps arm64 2:3.3.16-5ubuntu1 [229 kB] Get:98 http://ftpmaster.internal/ubuntu groovy/main arm64 openssl arm64 1.1.1f-1ubuntu3 [599 kB] Get:99 http://ftpmaster.internal/ubuntu groovy/main arm64 ca-certificates all 20190110ubuntu2 [145 kB] Get:100 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libsqlite3-0 arm64 3.32.3-1 [509 kB] Get:101 http://ftpmaster.internal/ubuntu groovy/main arm64 tzdata all 2020a-0ubuntu1 [293 kB] Get:102 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 xz-utils arm64 5.2.4-1ubuntu1 [81.2 kB] Get:103 http://ftpmaster.internal/ubuntu groovy/main arm64 libctf0 arm64 2.34.90.20200706-1ubuntu1 [43.2 kB] Get:104 http://ftpmaster.internal/ubuntu groovy/main arm64 binutils-aarch64-linux-gnu arm64 2.34.90.20200706-1ubuntu1 [2000 kB] Get:105 http://ftpmaster.internal/ubuntu groovy/main arm64 libbinutils arm64 2.34.90.20200706-1ubuntu1 [480 kB] Get:106 http://ftpmaster.internal/ubuntu groovy/main arm64 binutils arm64 2.34.90.20200706-1ubuntu1 [3360 B] Get:107 http://ftpmaster.internal/ubuntu groovy/main arm64 binutils-common arm64 2.34.90.20200706-1ubuntu1 [212 kB] Get:108 http://ftpmaster.internal/ubuntu groovy/main arm64 libctf-nobfd0 arm64 2.34.90.20200706-1ubuntu1 [44.1 kB] Get:109 http://ftpmaster.internal/ubuntu groovy/main arm64 make arm64 4.3-4ubuntu1 [158 kB] Get:110 http://ftpmaster.internal/ubuntu groovy/main arm64 dpkg-dev all 1.19.7ubuntu4 [679 kB] Get:111 http://ftpmaster.internal/ubuntu groovy/main arm64 libdpkg-perl all 1.19.7ubuntu4 [230 kB] Get:112 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 build-essential arm64 12.8ubuntu3 [4636 B] Get:113 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libasan5 arm64 9.3.0-15ubuntu1 [365 kB] Get:114 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 g++-9 arm64 9.3.0-15ubuntu1 [6821 kB] Get:115 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 gcc-9 arm64 9.3.0-15ubuntu1 [6695 kB] Get:116 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libstdc++-9-dev arm64 9.3.0-15ubuntu1 [1678 kB] Get:117 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libgcc-9-dev arm64 9.3.0-15ubuntu1 [918 kB] Get:118 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 cpp-9 arm64 9.3.0-15ubuntu1 [5970 kB] Get:119 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 gcc-9-base arm64 9.3.0-15ubuntu1 [19.6 kB] Get:120 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libmpfr6 arm64 4.1.0-3 [216 kB] Get:121 http://ftpmaster.internal/ubuntu groovy/main arm64 libassuan0 arm64 2.5.3-7.1 [33.1 kB] Get:122 http://ftpmaster.internal/ubuntu groovy/main arm64 pinentry-curses arm64 1.1.0-4build1 [34.4 kB] Get:123 http://ftpmaster.internal/ubuntu groovy/main arm64 libnpth0 arm64 1.6-2 [7644 B] Get:124 http://ftpmaster.internal/ubuntu groovy/main arm64 gpg arm64 2.2.20-1ubuntu1 [443 kB] Get:125 http://ftpmaster.internal/ubuntu groovy/main arm64 gpgconf arm64 2.2.20-1ubuntu1 [117 kB] Get:126 http://ftpmaster.internal/ubuntu groovy/main arm64 gpg-agent arm64 2.2.20-1ubuntu1 [216 kB] Get:127 http://ftpmaster.internal/ubuntu groovy/main arm64 pkgbinarymangler all 146 [31.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 63.7 MB in 4s (17.2 MB/s) (Reading database ... 12809 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.16-1ubuntu1_arm64.deb ... Unpacking libcrypt-dev:arm64 (1:4.4.16-1ubuntu1) over (1:4.4.10-10ubuntu4) ... Preparing to unpack .../libc6-dev_2.31-0ubuntu10_arm64.deb ... Unpacking libc6-dev:arm64 (2.31-0ubuntu10) over (2.31-0ubuntu9) ... Preparing to unpack .../libc-dev-bin_2.31-0ubuntu10_arm64.deb ... Unpacking libc-dev-bin (2.31-0ubuntu10) over (2.31-0ubuntu9) ... Preparing to unpack .../libcrypt1_1%3a4.4.16-1ubuntu1_arm64.deb ... Unpacking libcrypt1:arm64 (1:4.4.16-1ubuntu1) over (1:4.4.10-10ubuntu4) ... Setting up libcrypt1:arm64 (1:4.4.16-1ubuntu1) ... (Reading database ... 12808 files and directories currently installed.) Preparing to unpack .../0-linux-libc-dev_5.4.0-40.44_arm64.deb ... Unpacking linux-libc-dev:arm64 (5.4.0-40.44) over (5.4.0-26.30) ... Preparing to unpack .../1-libatomic1_10.1.0-3ubuntu1_arm64.deb ... Unpacking libatomic1:arm64 (10.1.0-3ubuntu1) over (10-20200411-0ubuntu1) ... 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Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up make (4.3-4ubuntu1) ... Setting up libmpfr6:arm64 (4.1.0-3) ... Setting up libncurses6:arm64 (6.2-1) ... Setting up xz-utils (5.2.4-1ubuntu1) ... Setting up libatomic1:arm64 (10.1.0-3ubuntu1) ... Setting up libss2:arm64 (1.45.6-1ubuntu1) ... Setting up libncursesw6:arm64 (6.2-1) ... Setting up logsave (1.45.6-1ubuntu1) ... Setting up libfdisk1:arm64 (2.35.2-7ubuntu3) ... Setting up libubsan1:arm64 (10.1.0-3ubuntu1) ... Setting up libcrypt-dev:arm64 (1:4.4.16-1ubuntu1) ... Setting up gpgconf (2.2.20-1ubuntu1) ... Setting up libperl5.30:arm64 (5.30.3-4) ... Setting up libbinutils:arm64 (2.34.90.20200706-1ubuntu1) ... Setting up libc-dev-bin (2.31-0ubuntu10) ... Setting up openssl (1.1.1f-1ubuntu3) ... Setting up libcc1-0:arm64 (10.1.0-3ubuntu1) ... Setting up gpg (2.2.20-1ubuntu1) ... Setting up liblsan0:arm64 (10.1.0-3ubuntu1) ... Setting up libprocps8:arm64 (2:3.3.16-5ubuntu1) ... Setting up libitm1:arm64 (10.1.0-3ubuntu1) ... Setting up gcc-9-base:arm64 (9.3.0-15ubuntu1) ... Setting up libtsan0:arm64 (10.1.0-3ubuntu1) ... Setting up libctf0:arm64 (2.34.90.20200706-1ubuntu1) ... Setting up pinentry-curses (1.1.0-4build1) ... Setting up gpg-agent (2.2.20-1ubuntu1) ... Setting up binutils-aarch64-linux-gnu (2.34.90.20200706-1ubuntu1) ... Setting up e2fsprogs (1.45.6-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up binutils (2.34.90.20200706-1ubuntu1) ... Setting up fdisk (2.35.2-7ubuntu3) ... Setting up ca-certificates (20190110ubuntu2) ... Updating certificates in /etc/ssl/certs... 0 added, 1 removed; done. Setting up libasan5:arm64 (9.3.0-15ubuntu1) ... Setting up perl (5.30.3-4) ... Setting up libdpkg-perl (1.19.7ubuntu4) ... Setting up procps (2:3.3.16-5ubuntu1) ... Installing new version of config file /etc/sysctl.conf ... Removing obsolete conffile /etc/sysctl.d/10-link-restrictions.conf ... Setting up cpp-9 (9.3.0-15ubuntu1) ... Setting up libc6-dev:arm64 (2.31-0ubuntu10) ... Setting up dpkg-dev (1.19.7ubuntu4) ... Setting up libgcc-9-dev:arm64 (9.3.0-15ubuntu1) ... Setting up build-essential (12.8ubuntu3) ... Setting up gcc-9 (9.3.0-15ubuntu1) ... Setting up libstdc++-9-dev:arm64 (9.3.0-15ubuntu1) ... Setting up g++-9 (9.3.0-15ubuntu1) ... Processing triggers for systemd (245.6-2ubuntu1) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... Processing triggers for ca-certificates (20190110ubuntu2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19591624 arm64 groovy-proposed -c chroot:build-PACKAGEBUILD-19591624 --arch=arm64 --dist=groovy-proposed --nolog bcftools_1.10.2-4.dsc Initiating build PACKAGEBUILD-19591624 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-079.buildd +==============================================================================+ | bcftools 1.10.2-4 (arm64) 15 Jul 2020 05:14 | +==============================================================================+ Package: bcftools Version: 1.10.2-4 Source Version: 1.10.2-4 Distribution: groovy-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/bcftools-41pH2y/bcftools-1.10.2' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-41pH2y' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19591624/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bcftools_1.10.2-4.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-Dtsi5v/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-Dtsi5v/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Dtsi5v/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Dtsi5v/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Dtsi5v/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-Dtsi5v/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (58.7 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libhogweed5 libnettle7 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Dtsi5v/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (59.6 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12822 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.10), libgsl-dev, tabix, libio-pty-perl Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.10), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<>/resolver-yNzDCc/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. Ign:1 copy:/<>/resolver-yNzDCc/apt_archive ./ InRelease Get:2 copy:/<>/resolver-yNzDCc/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-yNzDCc/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-yNzDCc/apt_archive ./ Sources [273 B] Get:5 copy:/<>/resolver-yNzDCc/apt_archive ./ Packages [580 B] Fetched 2972 B in 0s (85.3 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install bcftools build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libhogweed5 libnettle7 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbz2-dev libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl25 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db po-debconf tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbz2-dev libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl25 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db po-debconf sbuild-build-depends-bcftools-dummy tabix zlib1g-dev 0 upgraded, 68 newly installed, 0 to remove and 0 not upgraded. Need to get 26.7 MB of archives. After this operation, 94.4 MB of additional disk space will be used. Get:1 copy:/<>/resolver-yNzDCc/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [912 B] Get:2 http://ftpmaster.internal/ubuntu groovy/main arm64 bsdextrautils arm64 2.35.2-7ubuntu3 [73.8 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main arm64 libuchardet0 arm64 0.0.7-1 [68.0 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main arm64 groff-base arm64 1.22.4-5 [797 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main arm64 libpipeline1 arm64 1.5.2-2build1 [26.1 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main arm64 man-db arm64 2.9.3-2 [1100 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main arm64 libmagic-mgc arm64 1:5.38-5 [218 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main arm64 libmagic1 arm64 1:5.38-5 [71.6 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main arm64 file arm64 1:5.38-5 [23.3 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main arm64 libelf1 arm64 0.176-1.1build1 [44.2 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libglib2.0-0 arm64 2.64.4-1 [1198 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main arm64 libicu66 arm64 66.1-2ubuntu3 [8357 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main arm64 libxml2 arm64 2.9.10+dfsg-5 [572 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main arm64 gettext-base arm64 0.19.8.1-10build1 [48.2 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main arm64 libkrb5support0 arm64 1.17-10 [30.2 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main arm64 libk5crypto3 arm64 1.17-10 [80.3 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main arm64 libkeyutils1 arm64 1.6.1-2ubuntu1 [9932 B] Get:18 http://ftpmaster.internal/ubuntu groovy/main arm64 libkrb5-3 arm64 1.17-10 [312 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main arm64 libgssapi-krb5-2 arm64 1.17-10 [113 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main arm64 libpsl5 arm64 0.21.0-1.1 [51.4 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main arm64 libsigsegv2 arm64 2.12-2build1 [13.7 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main arm64 m4 arm64 1.4.18-4 [194 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main arm64 autoconf all 2.69-11.1 [321 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main arm64 autotools-dev all 20180224.1 [39.6 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main arm64 automake all 1:1.16.2-3ubuntu1 [548 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main arm64 autopoint all 0.19.8.1-10build1 [412 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main arm64 libtool all 2.4.6-14 [161 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main arm64 dh-autoreconf all 19 [16.1 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main arm64 libdebhelper-perl all 13.2ubuntu1 [64.2 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main arm64 libsub-override-perl all 0.09-2 [9532 B] Get:32 http://ftpmaster.internal/ubuntu groovy/main arm64 libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main arm64 dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:34 http://ftpmaster.internal/ubuntu groovy/main arm64 dwz arm64 0.13-5 [134 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main arm64 libcroco3 arm64 0.6.13-1 [77.1 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main arm64 gettext arm64 0.19.8.1-10build1 [850 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main arm64 po-debconf all 1.0.21 [233 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main arm64 debhelper all 13.2ubuntu1 [878 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main arm64 libroken18-heimdal arm64 7.7.0+dfsg-2 [39.4 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main arm64 libasn1-8-heimdal arm64 7.7.0+dfsg-2 [150 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main arm64 libbrotli1 arm64 1.0.7-6.1 [260 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main arm64 libbz2-dev arm64 1.0.8-3ubuntu1 [31.6 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main arm64 libheimbase1-heimdal arm64 7.7.0+dfsg-2 [27.9 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main arm64 libhcrypto4-heimdal arm64 7.7.0+dfsg-2 [84.8 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main arm64 libwind0-heimdal arm64 7.7.0+dfsg-2 [47.2 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main arm64 libhx509-5-heimdal arm64 7.7.0+dfsg-2 [98.6 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main arm64 libkrb5-26-heimdal arm64 7.7.0+dfsg-2 [192 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main arm64 libheimntlm0-heimdal arm64 7.7.0+dfsg-2 [14.8 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main arm64 libgssapi3-heimdal arm64 7.7.0+dfsg-2 [88.4 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2 [15.1 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2 [48.4 kB] Get:53 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libldap-common all 2.4.50+dfsg-1ubuntu3 [16.9 kB] Get:54 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libldap-2.4-2 arm64 2.4.50+dfsg-1ubuntu3 [146 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main arm64 libnghttp2-14 arm64 1.41.0-2 [62.6 kB] Get:56 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build2 [53.1 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main arm64 libssh-4 arm64 0.9.4-1ubuntu1 [159 kB] Get:58 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libcurl3-gnutls arm64 7.68.0-1ubuntu4 [211 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/universe arm64 libdeflate0 arm64 1.6-1 [51.1 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/universe arm64 libgslcblas0 arm64 2.6+dfsg-2 [56.2 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/universe arm64 libgsl25 arm64 2.6+dfsg-2 [787 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/universe arm64 libgsl-dev arm64 2.6+dfsg-2 [1007 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/universe arm64 libhts3 arm64 1.10.2-4 [316 kB] Get:64 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 liblzma-dev arm64 5.2.4-1ubuntu1 [144 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2ubuntu1 [154 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/universe arm64 libhts-dev arm64 1.10.2-4 [4830 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/main arm64 libio-pty-perl arm64 1:1.12-1 [31.5 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/universe arm64 tabix arm64 1.10.2-4 [326 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 26.7 MB in 1s (20.3 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 12822 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.35.2-7ubuntu3_arm64.deb ... Unpacking bsdextrautils (2.35.2-7ubuntu3) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-5_arm64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.2-2build1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.2-2build1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.3-2_arm64.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.38-5_arm64.deb ... Unpacking libmagic-mgc (1:5.38-5) ... 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Setting up libkeyutils1:arm64 (1.6.1-2ubuntu1) ... Setting up libpsl5:arm64 (0.21.0-1.1) ... Setting up bsdextrautils (2.35.2-7ubuntu3) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libgslcblas0:arm64 (2.6+dfsg-2) ... Setting up libio-pty-perl (1:1.12-1) ... Setting up libmagic-mgc (1:5.38-5) ... Setting up libgsl25:arm64 (2.6+dfsg-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:arm64 (2.64.4-1) ... No schema files found: doing nothing. Setting up libicu66:arm64 (66.1-2ubuntu3) ... Setting up libdebhelper-perl (13.2ubuntu1) ... Setting up libbrotli1:arm64 (1.0.7-6.1) ... Setting up libnghttp2-14:arm64 (1.41.0-2) ... Setting up libmagic1:arm64 (1:5.38-5) ... Setting up libdeflate0:arm64 (1.6-1) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-5) ... Setting up libldap-common (2.4.50+dfsg-1ubuntu3) ... Setting up libkrb5support0:arm64 (1.17-10) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build2) ... Setting up libsigsegv2:arm64 (2.12-2build1) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up libk5crypto3:arm64 (1.17-10) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2) ... Setting up libroken18-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up liblzma-dev:arm64 (5.2.4-1ubuntu1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2ubuntu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:arm64 (1.17-10) ... Setting up libelf1:arm64 (0.176-1.1build1) ... Setting up libxml2:arm64 (2.9.10+dfsg-5) ... Setting up libheimbase1-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libbz2-dev:arm64 (1.0.8-3ubuntu1) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libgsl-dev (2.6+dfsg-2) ... Setting up libtool (2.4.6-14) ... Setting up libasn1-8-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up m4 (1.4.18-4) ... Setting up libhcrypto4-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libwind0-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libgssapi-krb5-2:arm64 (1.17-10) ... Setting up libcroco3:arm64 (0.6.13-1) ... Setting up libssh-4:arm64 (0.9.4-1ubuntu1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up automake (1:1.16.2-3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10build1) ... Setting up libhx509-5-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libkrb5-26-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21) ... Setting up libheimntlm0-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libldap-2.4-2:arm64 (2.4.50+dfsg-1ubuntu3) ... Setting up libcurl3-gnutls:arm64 (7.68.0-1ubuntu4) ... Setting up tabix (1.10.2-4) ... Setting up libhts3:arm64 (1.10.2-4) ... Setting up libhts-dev:arm64 (1.10.2-4) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13.2ubuntu1) ... Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-177-generic arm64 (aarch64) Toolchain package versions: binutils_2.34.90.20200706-1ubuntu1 dpkg-dev_1.19.7ubuntu4 g++-9_9.3.0-15ubuntu1 gcc-9_9.3.0-15ubuntu1 libc6-dev_2.31-0ubuntu10 libstdc++-9-dev_9.3.0-15ubuntu1 libstdc++6_10.1.0-3ubuntu1 linux-libc-dev_5.4.0-40.44 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.7 autoconf_2.69-11.1 automake_1:1.16.2-3ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu9 base-passwd_3.5.47 bash_5.0-6ubuntu2 binutils_2.34.90.20200706-1ubuntu1 binutils-aarch64-linux-gnu_2.34.90.20200706-1ubuntu1 binutils-common_2.34.90.20200706-1ubuntu1 bsdextrautils_2.35.2-7ubuntu3 bsdutils_1:2.35.2-7ubuntu3 build-essential_12.8ubuntu3 bzip2_1.0.8-3ubuntu1 ca-certificates_20190110ubuntu2 coreutils_8.30-3ubuntu3 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-15ubuntu1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2ubuntu1 debianutils_4.11 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3build1 dpkg_1.19.7ubuntu4 dpkg-dev_1.19.7ubuntu4 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 fdisk_2.35.2-7ubuntu3 file_1:5.38-5 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-15ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10.1.0-3ubuntu1 gcc-9_9.3.0-15ubuntu1 gcc-9-base_9.3.0-15ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 init_1.58 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapparmor1_2.13.3-7ubuntu6 libapt-pkg6.0_2.1.7 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libasan5_9.3.0-15ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7.1 libatomic1_10.1.0-3ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.34.90.20200706-1ubuntu1 libblkid1_2.35.2-7ubuntu3 libbrotli1_1.0.7-6.1 libbz2-1.0_1.0.8-3ubuntu1 libbz2-dev_1.0.8-3ubuntu1 libc-bin_2.31-0ubuntu10 libc-dev-bin_2.31-0ubuntu10 libc6_2.31-0ubuntu10 libc6-dev_2.31-0ubuntu10 libcap-ng0_0.7.9-2.2 libcap2_1:2.36-1 libcc1-0_10.1.0-3ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1ubuntu1 libcrypt1_1:4.4.16-1ubuntu1 libcryptsetup12_2:2.3.3-1ubuntu3 libctf-nobfd0_2.34.90.20200706-1ubuntu1 libctf0_2.34.90.20200706-1ubuntu1 libcurl3-gnutls_7.68.0-1ubuntu4 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.252ubuntu1 libdebhelper-perl_13.2ubuntu1 libdeflate0_1.6-1 libdevmapper1.02.1_2:1.02.167-1ubuntu3 libdpkg-perl_1.19.7ubuntu4 libelf1_0.176-1.1build1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.24-1 libfdisk1_2.35.2-7ubuntu3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-9-dev_9.3.0-15ubuntu1 libgcc-s1_10.1.0-3ubuntu1 libgcrypt20_1.8.5-5ubuntu2 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.13-4ubuntu4 libgomp1_10.1.0-3ubuntu1 libgpg-error0_1.38-2 libgsl-dev_2.6+dfsg-2 libgsl25_2.6+dfsg-2 libgslcblas0_2.6+dfsg-2 libgssapi-krb5-2_1.17-10 libgssapi3-heimdal_7.7.0+dfsg-2 libhcrypto4-heimdal_7.7.0+dfsg-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed5_3.5.1+really3.5.1-2 libhogweed6_3.6-1build1 libhts-dev_1.10.2-4 libhts3_1.10.2-4 libhx509-5-heimdal_7.7.0+dfsg-2 libicu66_66.1-2ubuntu3 libidn2-0_2.3.0-1 libio-pty-perl_1:1.12-1 libip4tc2_1.8.4-3ubuntu2 libisl22_0.22.1-1 libitm1_10.1.0-3ubuntu1 libjson-c4_0.13.1+dfsg-9 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libldap-2.4-2_2.4.50+dfsg-1ubuntu3 libldap-common_2.4.50+dfsg-1ubuntu3 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_10.1.0-3ubuntu1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1ubuntu1 liblzma5_5.2.4-1ubuntu1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-7ubuntu3 libmpc3_1.1.0-1 libmpfr6_4.1.0-3 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnettle8_3.6-1build1 libnghttp2-14_1.41.0-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu5 libpam-modules-bin_1.3.1-5ubuntu5 libpam-runtime_1.3.1-5ubuntu5 libpam0g_1.3.1-5ubuntu5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libprocps8_2:3.3.16-5ubuntu1 libpsl5_0.21.0-1.1 libreadline8_8.0-4 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1ubuntu4 libselinux1_3.1-1 libsemanage-common_3.0-1build2 libsemanage1_3.0-1build2 libsepol1_3.1-1 libsigsegv2_2.12-2build1 libsmartcols1_2.35.2-7ubuntu3 libsqlite3-0_3.32.3-1 libss2_1.45.6-1ubuntu1 libssh-4_0.9.4-1ubuntu1 libssl1.1_1.1.1f-1ubuntu3 libstdc++-9-dev_9.3.0-15ubuntu1 libstdc++6_10.1.0-3ubuntu1 libsub-override-perl_0.09-2 libsystemd0_245.6-2ubuntu1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10.1.0-3ubuntu1 libubsan1_10.1.0-3ubuntu1 libuchardet0_0.0.7-1 libudev1_245.6-2ubuntu1 libunistring2_0.9.10-4 libuuid1_2.35.2-7ubuntu3 libwind0-heimdal_7.7.0+dfsg-2 libxml2_2.9.10+dfsg-5 libzstd1_1.4.5+dfsg-3 linux-libc-dev_5.4.0-40.44 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu6 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.35.2-7ubuntu3 ncurses-base_6.2-1 ncurses-bin_6.2-1 openssl_1.1.1f-1ubuntu3 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4build1 pkgbinarymangler_146 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu1 readline-common_8.0-4 sbuild-build-depends-bcftools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1build1 sensible-utils_0.0.12+nmu1 systemd_245.6-2ubuntu1 systemd-sysv_245.6-2ubuntu1 systemd-timesyncd_245.6-2ubuntu1 sysvinit-utils_2.96-3ubuntu1 tabix_1.10.2-4 tar_1.30+dfsg-7 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.35.2-7ubuntu3 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Jul 14 20:43:08 2020 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcftools_1.10.2-4.dsc dpkg-source: info: extracting bcftools in bcftools-1.10.2 dpkg-source: info: unpacking bcftools_1.10.2.orig.tar.gz dpkg-source: info: unpacking bcftools_1.10.2-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying skip_new_test_failing_on_32bit.patch dpkg-source: info: applying 2to3.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19591624 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19591624 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19591624 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.10.2-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean rm -f config.mk && touch config.mk dh clean dh_auto_clean make -j4 distclean make[1]: Entering directory '/<>' rm -f test/*.o test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f test/*.hex rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/<>' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf 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 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 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 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 make[1]: Leaving directory '/<>' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/aarch64-linux-gnu/bcftools ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/aarch64-linux-gnu/bcftools checking for 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... /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... -ldl checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/<>' dh_auto_build -a make -j4 make[1]: Entering directory '/<>' echo '#define BCFTOOLS_VERSION "1.10.2"' > version.h gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/aarch64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/add-variantkey.so version.c plugins/add-variantkey.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/allele-length.so version.c plugins/allele-length.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/gvcfz.so version.c plugins/gvcfz.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/indel-stats.so version.c plugins/indel-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/parental-origin.so version.c plugins/parental-origin.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/split-vep.so version.c plugins/split-vep.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/split.so version.c plugins/split.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/trio-dnm.so version.c plugins/trio-dnm.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c -ldl gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -ldl -ldl gcc -rdynamic -pthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o ccall.o em.o prob1.o kmin.o vcfplugin.o -lhts -lm -lz -ldl -ldl make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/<>' ./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 --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/R8t1ULGUU2/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/R8t1ULGUU2/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/R8t1ULGUU2/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/R8t1ULGUU2/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/R8t1ULGUU2/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/R8t1ULGUU2/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/R8t1ULGUU2/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/R8t1ULGUU2/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/R8t1ULGUU2/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/R8t1ULGUU2/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/R8t1ULGUU2/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/R8t1ULGUU2/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/R8t1ULGUU2/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/R8t1ULGUU2/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/R8t1ULGUU2/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/R8t1ULGUU2/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/R8t1ULGUU2/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/R8t1ULGUU2/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/R8t1ULGUU2/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/R8t1ULGUU2/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/R8t1ULGUU2/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/R8t1ULGUU2/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/R8t1ULGUU2/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/R8t1ULGUU2/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/R8t1ULGUU2/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/R8t1ULGUU2/empty.bcf .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/R8t1ULGUU2/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/check.vcf.gz | /<>/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /<>/misc/plot-vcfstats -m /tmp/R8t1ULGUU2/check.1.chk /tmp/R8t1ULGUU2/check.2.chk /tmp/R8t1ULGUU2/check.3.chk /tmp/R8t1ULGUU2/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/R8t1ULGUU2/stats.a.vcf.gz /tmp/R8t1ULGUU2/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/R8t1ULGUU2/stats.a.vcf.gz /tmp/R8t1ULGUU2/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/R8t1ULGUU2/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/R8t1ULGUU2/isec.a.vcf.gz /tmp/R8t1ULGUU2/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/R8t1ULGUU2/isec.a.vcf.gz /tmp/R8t1ULGUU2/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/R8t1ULGUU2/isec.a.vcf.gz /tmp/R8t1ULGUU2/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/R8t1ULGUU2/isec.a.vcf.gz /tmp/R8t1ULGUU2/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/R8t1ULGUU2/isec.a.vcf.gz /tmp/R8t1ULGUU2/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/R8t1ULGUU2/isec.a.vcf.gz /tmp/R8t1ULGUU2/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/R8t1ULGUU2/isec.a.vcf.gz /tmp/R8t1ULGUU2/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/R8t1ULGUU2/isec.a.vcf.gz /tmp/R8t1ULGUU2/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/R8t1ULGUU2/isec.a.vcf.gz /tmp/R8t1ULGUU2/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/R8t1ULGUU2/isec.a.vcf.gz /tmp/R8t1ULGUU2/isec.b.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/R8t1ULGUU2/isec.tab.gz /tmp/R8t1ULGUU2/isec.a.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/R8t1ULGUU2/isec.tab.gz /tmp/R8t1ULGUU2/isec.a.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /<>/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/R8t1ULGUU2/isec-miss.1.1.vcf.gz /tmp/R8t1ULGUU2/isec-miss.1.2.vcf.gz /tmp/R8t1ULGUU2/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/R8t1ULGUU2/isec-miss.1.1.vcf.gz /tmp/R8t1ULGUU2/isec-miss.1.2.vcf.gz /tmp/R8t1ULGUU2/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/R8t1ULGUU2/isec-miss.1.1.vcf.gz /tmp/R8t1ULGUU2/isec-miss.1.2.vcf.gz /tmp/R8t1ULGUU2/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/R8t1ULGUU2/isec-miss.1.1.vcf.gz /tmp/R8t1ULGUU2/isec-miss.1.2.vcf.gz /tmp/R8t1ULGUU2/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/R8t1ULGUU2/isec-miss.2.1.vcf.gz /tmp/R8t1ULGUU2/isec-miss.2.2.vcf.gz /tmp/R8t1ULGUU2/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/R8t1ULGUU2/isec-miss.2.1.vcf.gz /tmp/R8t1ULGUU2/isec-miss.2.2.vcf.gz /tmp/R8t1ULGUU2/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/R8t1ULGUU2/isec-miss.2.1.vcf.gz /tmp/R8t1ULGUU2/isec-miss.2.2.vcf.gz /tmp/R8t1ULGUU2/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/R8t1ULGUU2/isec-miss.2.1.vcf.gz /tmp/R8t1ULGUU2/isec-miss.2.2.vcf.gz /tmp/R8t1ULGUU2/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/R8t1ULGUU2/merge.a.vcf.gz /tmp/R8t1ULGUU2/merge.b.vcf.gz /tmp/R8t1ULGUU2/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/R8t1ULGUU2/merge.a.vcf.gz /tmp/R8t1ULGUU2/merge.b.vcf.gz /tmp/R8t1ULGUU2/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/R8t1ULGUU2/merge.a.vcf.gz /tmp/R8t1ULGUU2/merge.b.vcf.gz /tmp/R8t1ULGUU2/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -Fx /tmp/R8t1ULGUU2/merge.a.vcf.gz /tmp/R8t1ULGUU2/merge.b.vcf.gz /tmp/R8t1ULGUU2/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/R8t1ULGUU2/merge.a.vcf.gz /tmp/R8t1ULGUU2/merge.b.vcf.gz /tmp/R8t1ULGUU2/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -0 /tmp/R8t1ULGUU2/merge.a.vcf.gz /tmp/R8t1ULGUU2/merge.b.vcf.gz /tmp/R8t1ULGUU2/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/R8t1ULGUU2/merge.2.a.vcf.gz /tmp/R8t1ULGUU2/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m none /tmp/R8t1ULGUU2/merge.2.a.vcf.gz /tmp/R8t1ULGUU2/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/R8t1ULGUU2/merge.2.a.vcf.gz /tmp/R8t1ULGUU2/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m both /tmp/R8t1ULGUU2/merge.2.a.vcf.gz /tmp/R8t1ULGUU2/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/R8t1ULGUU2/merge.2.a.vcf.gz /tmp/R8t1ULGUU2/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m all /tmp/R8t1ULGUU2/merge.2.a.vcf.gz /tmp/R8t1ULGUU2/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/R8t1ULGUU2/merge.3.a.vcf.gz /tmp/R8t1ULGUU2/merge.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/R8t1ULGUU2/merge.3.a.vcf.gz /tmp/R8t1ULGUU2/merge.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/R8t1ULGUU2/merge.4.a.vcf.gz /tmp/R8t1ULGUU2/merge.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m id /tmp/R8t1ULGUU2/merge.4.a.vcf.gz /tmp/R8t1ULGUU2/merge.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/R8t1ULGUU2/gvcf.merge.1.vcf.gz /tmp/R8t1ULGUU2/gvcf.merge.2.vcf.gz /tmp/R8t1ULGUU2/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/R8t1ULGUU2/gvcf.merge.1.vcf.gz /tmp/R8t1ULGUU2/gvcf.merge.2.vcf.gz /tmp/R8t1ULGUU2/gvcf.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/R8t1ULGUU2/merge.gvcf.2.a.vcf.gz /tmp/R8t1ULGUU2/merge.gvcf.2.b.vcf.gz /tmp/R8t1ULGUU2/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/R8t1ULGUU2/merge.gvcf.2.a.vcf.gz /tmp/R8t1ULGUU2/merge.gvcf.2.b.vcf.gz /tmp/R8t1ULGUU2/merge.gvcf.2.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - -i SRC:join /tmp/R8t1ULGUU2/merge.gvcf.3.a.vcf.gz /tmp/R8t1ULGUU2/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/R8t1ULGUU2/merge.gvcf.3.a.vcf.gz /tmp/R8t1ULGUU2/merge.gvcf.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/R8t1ULGUU2/merge.gvcf.4.a.vcf.gz /tmp/R8t1ULGUU2/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/R8t1ULGUU2/merge.gvcf.4.a.vcf.gz /tmp/R8t1ULGUU2/merge.gvcf.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/R8t1ULGUU2/merge.5.a.vcf.gz /tmp/R8t1ULGUU2/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/R8t1ULGUU2/merge.5.a.vcf.gz /tmp/R8t1ULGUU2/merge.5.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/R8t1ULGUU2/merge.6.a.vcf.gz /tmp/R8t1ULGUU2/merge.6.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/R8t1ULGUU2/merge.6.a.vcf.gz /tmp/R8t1ULGUU2/merge.6.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/R8t1ULGUU2/merge.gvcf.7.a.vcf.gz /tmp/R8t1ULGUU2/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/R8t1ULGUU2/merge.gvcf.7.a.vcf.gz /tmp/R8t1ULGUU2/merge.gvcf.7.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/R8t1ULGUU2/merge.gvcf.8.a.vcf.gz /tmp/R8t1ULGUU2/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/R8t1ULGUU2/merge.gvcf.8.a.vcf.gz /tmp/R8t1ULGUU2/merge.gvcf.8.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/R8t1ULGUU2/merge.7.a.vcf.gz /tmp/R8t1ULGUU2/merge.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/R8t1ULGUU2/merge.7.a.vcf.gz /tmp/R8t1ULGUU2/merge.7.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/R8t1ULGUU2/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.vcf.gz | /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /<>/bcftools query -f '%RSX\t%VKX\n' /tmp/R8t1ULGUU2/query.variantkey.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.variantkey.vcf.gz | /<>/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /<>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/R8t1ULGUU2/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.vcf.gz | /<>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /<>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/R8t1ULGUU2/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.vcf.gz | /<>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /<>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/R8t1ULGUU2/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.vcf.gz | /<>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/R8t1ULGUU2/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.vcf.gz | /<>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /<>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/R8t1ULGUU2/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/R8t1ULGUU2/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/R8t1ULGUU2/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/R8t1ULGUU2/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /<>/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/R8t1ULGUU2/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.vectors.vcf.gz | /<>/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: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/R8t1ULGUU2/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/R8t1ULGUU2/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/R8t1ULGUU2/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/R8t1ULGUU2/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/R8t1ULGUU2/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.2.vcf.gz | /<>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/R8t1ULGUU2/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/R8t1ULGUU2/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/R8t1ULGUU2/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/R8t1ULGUU2/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/R8t1ULGUU2/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/R8t1ULGUU2/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /<>/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/R8t1ULGUU2/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/filter-missing-floats.vcf.gz | /<>/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: /<>/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/R8t1ULGUU2/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/filter-missing-floats.vcf.gz | /<>/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: /<>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/R8t1ULGUU2/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/missing.vcf.gz | /<>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /<>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/R8t1ULGUU2/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.2.vcf.gz | /<>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/R8t1ULGUU2/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/filter.5.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/R8t1ULGUU2/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/filter.5.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/R8t1ULGUU2/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.3.vcf.gz | /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/R8t1ULGUU2/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.3.vcf.gz | /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /<>/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/R8t1ULGUU2/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.3.vcf.gz | /<>/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/R8t1ULGUU2/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/filter.5.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/R8t1ULGUU2/query.filter.4.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.4.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /<>/bcftools query -f'%ID\n' -i 'ID=@/<>/test/query.56.out' /tmp/R8t1ULGUU2/view.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.vcf.gz | /<>/bcftools query -f'%ID\n' -i 'ID=@/<>/test/query.56.out' .. ok test_vcf_query: /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/R8t1ULGUU2/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.5.vcf.gz | /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/R8t1ULGUU2/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.5.vcf.gz | /<>/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: /<>/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/R8t1ULGUU2/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.5.vcf.gz | /<>/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /<>/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/R8t1ULGUU2/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.vcf.gz | /<>/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/R8t1ULGUU2/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.negative.vcf.gz | /<>/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/R8t1ULGUU2/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.negative.vcf.gz | /<>/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/R8t1ULGUU2/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.negative.vcf.gz | /<>/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/R8t1ULGUU2/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.negative.vcf.gz | /<>/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /<>/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/R8t1ULGUU2/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.vcf.gz | /<>/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /<>/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/R8t1ULGUU2/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.vcf.gz | /<>/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /<>/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/R8t1ULGUU2/query.filter.6.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.6.vcf.gz | /<>/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/R8t1ULGUU2/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/R8t1ULGUU2/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/R8t1ULGUU2/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/R8t1ULGUU2/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/R8t1ULGUU2/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/R8t1ULGUU2/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/R8t1ULGUU2/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/R8t1ULGUU2/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/R8t1ULGUU2/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.8.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/R8t1ULGUU2/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.8.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/R8t1ULGUU2/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.9.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/R8t1ULGUU2/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.9.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /<>/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/R8t1ULGUU2/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.10.vcf.gz | /<>/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /<>/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/R8t1ULGUU2/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/query.filter.10.vcf.gz | /<>/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_norm: /<>/bcftools norm --no-version -cx -f /<>/test/norm.fa /tmp/R8t1ULGUU2/norm.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -cx -f /<>/test/norm.fa /tmp/R8t1ULGUU2/norm.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/R8t1ULGUU2/norm.split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/R8t1ULGUU2/norm.split.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/R8t1ULGUU2/norm.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/R8t1ULGUU2/norm.split.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --force /tmp/R8t1ULGUU2/norm.split.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- --force /tmp/R8t1ULGUU2/norm.split.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- -f /<>/test/norm.fa /tmp/R8t1ULGUU2/norm.split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- -f /<>/test/norm.fa /tmp/R8t1ULGUU2/norm.split.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/R8t1ULGUU2/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/R8t1ULGUU2/norm.merge.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/R8t1ULGUU2/norm.merge.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/R8t1ULGUU2/norm.merge.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/R8t1ULGUU2/norm.merge.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/R8t1ULGUU2/norm.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/R8t1ULGUU2/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ -s /tmp/R8t1ULGUU2/norm.merge.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -Nc s -f /<>/test/norm.fa /tmp/R8t1ULGUU2/norm.setref.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -Nc s -f /<>/test/norm.fa /tmp/R8t1ULGUU2/norm.setref.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.fa /tmp/R8t1ULGUU2/norm.telomere.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/R8t1ULGUU2/norm.telomere.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/R8t1ULGUU2/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d snps /tmp/R8t1ULGUU2/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/R8t1ULGUU2/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d indels /tmp/R8t1ULGUU2/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/R8t1ULGUU2/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d both /tmp/R8t1ULGUU2/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/R8t1ULGUU2/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d all /tmp/R8t1ULGUU2/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/R8t1ULGUU2/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d none /tmp/R8t1ULGUU2/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/R8t1ULGUU2/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d exact /tmp/R8t1ULGUU2/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/R8t1ULGUU2/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d none /tmp/R8t1ULGUU2/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/R8t1ULGUU2/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d exact /tmp/R8t1ULGUU2/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/R8t1ULGUU2/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d indels /tmp/R8t1ULGUU2/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d any /tmp/R8t1ULGUU2/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d any /tmp/R8t1ULGUU2/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/R8t1ULGUU2/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d both /tmp/R8t1ULGUU2/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/R8t1ULGUU2/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d snps /tmp/R8t1ULGUU2/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.2.fa /tmp/R8t1ULGUU2/norm.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.2.fa /tmp/R8t1ULGUU2/norm.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/R8t1ULGUU2/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/R8t1ULGUU2/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/R8t1ULGUU2/view.vcf.gz -r20,Y .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/R8t1ULGUU2/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/R8t1ULGUU2/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/R8t1ULGUU2/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/R8t1ULGUU2/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/R8t1ULGUU2/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -p /tmp/R8t1ULGUU2/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/R8t1ULGUU2/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -P /tmp/R8t1ULGUU2/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/R8t1ULGUU2/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/R8t1ULGUU2/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/R8t1ULGUU2/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/R8t1ULGUU2/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/R8t1ULGUU2/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/R8t1ULGUU2/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/R8t1ULGUU2/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/R8t1ULGUU2/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/R8t1ULGUU2/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/R8t1ULGUU2/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/R8t1ULGUU2/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/R8t1ULGUU2/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/R8t1ULGUU2/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/R8t1ULGUU2/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/R8t1ULGUU2/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/R8t1ULGUU2/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/R8t1ULGUU2/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/R8t1ULGUU2/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asB /tmp/R8t1ULGUU2/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/R8t1ULGUU2/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/R8t1ULGUU2/view.vectors.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/R8t1ULGUU2/view.vectors.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/R8t1ULGUU2/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/R8t1ULGUU2/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/R8t1ULGUU2/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/R8t1ULGUU2/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/R8t1ULGUU2/filter.2.vcf.gz 1:3062917-3157410 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/R8t1ULGUU2/idx.1.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/R8t1ULGUU2/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.2.bed /tmp/R8t1ULGUU2/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.3.bed /tmp/R8t1ULGUU2/idx.3.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.4.bed /tmp/R8t1ULGUU2/idx.4.vcf.gz .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.1.vcf | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.1.vcf -Ou | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.2.vcf | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.2.vcf -Ou | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.3.vcf | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.4.vcf | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.4.vcf -Ou | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.5.vcf | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.5.vcf -Ou | /<>/bcftools view -H .. ok test_vcf_filter: /<>/bcftools filter -S. -e'TXT0="text"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'TXT0="text"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/STR="XX"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/STR="XX"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FILTER="aaa"' /<>/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /<>/test/view.filter.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -H -C5:nonmajor /tmp/R8t1ULGUU2/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/R8t1ULGUU2/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/R8t1ULGUU2/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/R8t1ULGUU2/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/R8t1ULGUU2/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/R8t1ULGUU2/view.filter.annovar.vcf.gz .. ok test_vcf_call: /<>/bcftools call --no-version -mv /<>/test/mpileup.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mg0 /<>/test/mpileup.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mg0 /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -S /<>/test/mpileup.3.samples /<>/test/mpileup.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -S /<>/test/mpileup.3.samples /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -S /<>/test/mpileup.4.samples /<>/test/mpileup.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -S /<>/test/mpileup.4.samples /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -S /<>/test/mpileup.5.samples /<>/test/mpileup.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -S /<>/test/mpileup.5.samples /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.X.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.X.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.X.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.X.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.X.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.X.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv /<>/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv /<>/test/mpileup.NA19213.NA19129.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -G - /<>/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -G - /<>/test/mpileup.NA19213.NA19129.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv /<>/test/mpileup.hwe.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv /<>/test/mpileup.hwe.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -G - /<>/test/mpileup.hwe.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -G - /<>/test/mpileup.hwe.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -G /<>/test/mpileup.hwe.samples /<>/test/mpileup.hwe.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -G /<>/test/mpileup.hwe.samples /<>/test/mpileup.hwe.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.tab.gz /<>/test/mpileup.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.tab.gz /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.2.tab.gz /<>/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.2.tab.gz /<>/test/mpileup.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.3.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.3.tab.gz -i /<>/test/mpileup.3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.4.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.4.tab.gz -i /<>/test/mpileup.3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.5.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.5.tab.gz -i /<>/test/mpileup.3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.6.tab.gz -i /<>/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.6.tab.gz -i /<>/test/mpileup.4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.7.tab.gz -i /<>/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.7.tab.gz -i /<>/test/mpileup.5.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.cals.1.tab.gz /<>/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.cals.1.tab.gz /<>/test/mpileup.cals.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.cals.2.tab.gz /<>/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/R8t1ULGUU2/mpileup.cals.2.tab.gz /<>/test/mpileup.cals.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv /<>/test/mpileup.c.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -cv /<>/test/mpileup.c.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.c.X.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.c.X.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.c.X.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.c.X.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.c.X.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.c.X.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -mx -g2 -G2 /<>/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -mx -g2 -G2 /<>/test/filter.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<>/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<>/test/filter.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -e'INFO/DP=19' /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'INFO/DP=19' /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'INFO/DP=19' -s XX /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'INFO/DP=19' -s XX /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'INFO/DP=19' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'INFO/DP=19' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'INFO/DP=19' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'ALT="."' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'ALT="."' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -S . -i 'FORMAT/TEST3<25' /<>/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /<>/test/filter.4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -i 'FORMAT/TEST4<25' /<>/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /<>/test/filter.4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i'GT="A"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="A"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="RR"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="RR"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="RA"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="RA"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="AR"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="AR"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="AA"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="AA"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="aA"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="aA"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="Aa"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="Aa"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="HOM"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="HOM"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="HET"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="HET"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="HAP"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="HAP"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[:1]=11' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[:1]=11' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[1:]=11' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[1:]=11' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'FR[0:1]=11' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'FR[0:1]=11' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[*]="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[*]="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[0:0]=="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[0:0]=="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[0:0]!="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[0:0]!="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'QUAL=="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'QUAL=="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /<>/bcftools filter -i'N_PASS(DP>32)=1' /<>/test/filter.2.vcf | /<>/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'N_PASS(DP>32)=1' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /<>/bcftools filter -i'F_PASS(DP>32)=0.5' /<>/test/filter.2.vcf | /<>/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /<>/bcftools filter -i'F_MISSING>=1/5' /<>/test/filter.6.vcf | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'F_MISSING>=1/5' /<>/test/filter.6.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -i'F_MISSING>=0.2' /<>/test/filter.6.vcf | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'F_MISSING>=0.2' /<>/test/filter.6.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /<>/test/filter.6.vcf | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /<>/test/filter.6.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /<>/test/filter.6.vcf | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /<>/test/filter.6.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\n' .. ok test_vcf_sort: /<>/bcftools sort -m 0 /<>/test/sort.vcf | /<>/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /<>/bcftools sort -Ob -m 0 /<>/test/sort.vcf | /<>/bcftools view | /<>/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /<>/bcftools sort -m 1000 /<>/test/sort.vcf | /<>/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /<>/bcftools sort -Ob -m 1000 /<>/test/sort.vcf | /<>/bcftools view | /<>/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab /tmp/R8t1ULGUU2/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /<>/test/regions.tab /tmp/R8t1ULGUU2/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/R8t1ULGUU2/regions.tab.gz /tmp/R8t1ULGUU2/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/R8t1ULGUU2/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/R8t1ULGUU2/regions.tab.gz /tmp/R8t1ULGUU2/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/R8t1ULGUU2/regions.bed /tmp/R8t1ULGUU2/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/R8t1ULGUU2/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/R8t1ULGUU2/regions.bed /tmp/R8t1ULGUU2/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/R8t1ULGUU2/regions.bed.gz /tmp/R8t1ULGUU2/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/R8t1ULGUU2/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/R8t1ULGUU2/regions.bed.gz /tmp/R8t1ULGUU2/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,-,T_STR /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,-,T_STR /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/R8t1ULGUU2/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/R8t1ULGUU2/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<>/test/annotate3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<>/test/annotate3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x FORMAT /<>/test/annotate3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x FORMAT /<>/test/annotate3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots4.vcf.gz -c +INFO /tmp/R8t1ULGUU2/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots4.vcf.gz -c +INFO /tmp/R8t1ULGUU2/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots10.tab.gz -h /<>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<>/test/annotate10.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots10.tab.gz -h /<>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<>/test/annotate10.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<>/test/annotate2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<>/test/annotate2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots11.vcf.gz -c FMT /tmp/R8t1ULGUU2/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots11.vcf.gz -c FMT /tmp/R8t1ULGUU2/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c FMT/newGT:=GT /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots2.vcf.gz -c FMT/newGT:=GT /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots12.vcf.gz -c FMT/GT:=newGT /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots12.vcf.gz -c FMT/GT:=newGT /tmp/R8t1ULGUU2/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots13.tab.gz -h /<>/test/annotate13.hdr -c CHROM,BEG,END,ABC /<>/test/annotate13.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots13.tab.gz -h /<>/test/annotate13.hdr -c CHROM,BEG,END,ABC /<>/test/annotate13.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots13.tab.gz -h /<>/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /<>/test/annotate13.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots13.tab.gz -h /<>/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /<>/test/annotate13.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots13.tab.gz -h /<>/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /<>/test/annotate13.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots13.tab.gz -h /<>/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /<>/test/annotate13.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x FILTER/XX,INFO/XX --force /<>/test/annotate14.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /<>/test/annotate14.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annotate15.tab.gz -h /<>/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /<>/test/annotate15.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annotate15.tab.gz -h /<>/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /<>/test/annotate15.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annotate15.tab.gz -h /<>/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /<>/test/annotate15.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annotate15.tab.gz -h /<>/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /<>/test/annotate15.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x FILTER /<>/test/annotate16.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x FILTER /<>/test/annotate16.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /<>/test/annotate17.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /<>/test/annotate17.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /<>/test/annotate17.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /<>/test/annotate17.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /<>/test/annotate17.3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /<>/test/annotate17.3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /<>/test/annotate18.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /<>/test/annotate18.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /<>/test/annotate18.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /<>/test/annotate18.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R8t1ULGUU2/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R8t1ULGUU2/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/R8t1ULGUU2/concat.1.a.vcf.gz /tmp/R8t1ULGUU2/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/R8t1ULGUU2/concat.1.a.vcf.gz /tmp/R8t1ULGUU2/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/R8t1ULGUU2/concat.1.a.bcf /tmp/R8t1ULGUU2/concat.1.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/R8t1ULGUU2/concat.1.a.bcf /tmp/R8t1ULGUU2/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/R8t1ULGUU2/concat.2.a.vcf.gz /tmp/R8t1ULGUU2/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/R8t1ULGUU2/concat.2.a.vcf.gz /tmp/R8t1ULGUU2/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/R8t1ULGUU2/concat.2.a.bcf /tmp/R8t1ULGUU2/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/R8t1ULGUU2/concat.2.a.bcf /tmp/R8t1ULGUU2/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/R8t1ULGUU2/concat.2.a.vcf.gz /tmp/R8t1ULGUU2/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/R8t1ULGUU2/concat.2.a.vcf.gz /tmp/R8t1ULGUU2/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/R8t1ULGUU2/concat.2.a.bcf /tmp/R8t1ULGUU2/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/R8t1ULGUU2/concat.2.a.bcf /tmp/R8t1ULGUU2/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/R8t1ULGUU2/concat.3.a.vcf.gz /tmp/R8t1ULGUU2/concat.3.b.vcf.gz /tmp/R8t1ULGUU2/concat.3.0.vcf.gz /tmp/R8t1ULGUU2/concat.3.c.vcf.gz /tmp/R8t1ULGUU2/concat.3.d.vcf.gz /tmp/R8t1ULGUU2/concat.3.e.vcf.gz /tmp/R8t1ULGUU2/concat.3.f.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/R8t1ULGUU2/concat.3.a.vcf.gz /tmp/R8t1ULGUU2/concat.3.b.vcf.gz /tmp/R8t1ULGUU2/concat.3.0.vcf.gz /tmp/R8t1ULGUU2/concat.3.c.vcf.gz /tmp/R8t1ULGUU2/concat.3.d.vcf.gz /tmp/R8t1ULGUU2/concat.3.e.vcf.gz /tmp/R8t1ULGUU2/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/R8t1ULGUU2/concat.3.a.bcf /tmp/R8t1ULGUU2/concat.3.b.bcf /tmp/R8t1ULGUU2/concat.3.0.bcf /tmp/R8t1ULGUU2/concat.3.c.bcf /tmp/R8t1ULGUU2/concat.3.d.bcf /tmp/R8t1ULGUU2/concat.3.e.bcf /tmp/R8t1ULGUU2/concat.3.f.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/R8t1ULGUU2/concat.3.a.bcf /tmp/R8t1ULGUU2/concat.3.b.bcf /tmp/R8t1ULGUU2/concat.3.0.bcf /tmp/R8t1ULGUU2/concat.3.c.bcf /tmp/R8t1ULGUU2/concat.3.d.bcf /tmp/R8t1ULGUU2/concat.3.e.bcf /tmp/R8t1ULGUU2/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1213716676 .. ok test_naive_concat: /<>/bcftools concat --naive-force /tmp/R8t1ULGUU2/naive_concat.0.bcf /tmp/R8t1ULGUU2/naive_concat.1.bcf /tmp/R8t1ULGUU2/naive_concat.2.bcf /tmp/R8t1ULGUU2/naive_concat.3.bcf /tmp/R8t1ULGUU2/naive_concat.4.bcf /tmp/R8t1ULGUU2/naive_concat.5.bcf /tmp/R8t1ULGUU2/naive_concat.6.bcf /tmp/R8t1ULGUU2/naive_concat.7.bcf /tmp/R8t1ULGUU2/naive_concat.8.bcf /tmp/R8t1ULGUU2/naive_concat.9.bcf | /<>/bcftools view -H .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/R8t1ULGUU2/naive_concat.0.vcf.gz /tmp/R8t1ULGUU2/naive_concat.1.vcf.gz /tmp/R8t1ULGUU2/naive_concat.2.vcf.gz /tmp/R8t1ULGUU2/naive_concat.3.vcf.gz /tmp/R8t1ULGUU2/naive_concat.4.vcf.gz /tmp/R8t1ULGUU2/naive_concat.5.vcf.gz /tmp/R8t1ULGUU2/naive_concat.6.vcf.gz /tmp/R8t1ULGUU2/naive_concat.7.vcf.gz /tmp/R8t1ULGUU2/naive_concat.8.vcf.gz /tmp/R8t1ULGUU2/naive_concat.9.vcf.gz | /<>/bcftools view -H .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/R8t1ULGUU2/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R8t1ULGUU2/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/R8t1ULGUU2/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R8t1ULGUU2/reheader.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/R8t1ULGUU2/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R8t1ULGUU2/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/R8t1ULGUU2/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R8t1ULGUU2/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/R8t1ULGUU2/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R8t1ULGUU2/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/R8t1ULGUU2/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R8t1ULGUU2/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/R8t1ULGUU2/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R8t1ULGUU2/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/R8t1ULGUU2/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R8t1ULGUU2/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/R8t1ULGUU2/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R8t1ULGUU2/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/R8t1ULGUU2/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R8t1ULGUU2/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /<>/test/empty.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/empty.vcf | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /tmp/R8t1ULGUU2/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R8t1ULGUU2/empty.bcf | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /tmp/R8t1ULGUU2/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R8t1ULGUU2/empty.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.fai /<>/test/reheader.2.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.fai /tmp/R8t1ULGUU2/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.fai /tmp/R8t1ULGUU2/reheader.2.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.2.hdr -f /<>/test/reheader.fai /<>/test/reheader.2.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.2.hdr -f /<>/test/reheader.fai /tmp/R8t1ULGUU2/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.2.hdr -f /<>/test/reheader.fai /tmp/R8t1ULGUU2/reheader.2.vcf.gz | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/R8t1ULGUU2/rename.map -Ov /tmp/R8t1ULGUU2/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/R8t1ULGUU2/rename.map -Ob /tmp/R8t1ULGUU2/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/R8t1ULGUU2/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/R8t1ULGUU2/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/R8t1ULGUU2/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/convert.vcf.gz | /<>/bcftools convert -g -,. .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/R8t1ULGUU2/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/convert.vcf.gz | /<>/bcftools convert -g .,- .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/R8t1ULGUU2/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/R8t1ULGUU2/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/R8t1ULGUU2/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/R8t1ULGUU2/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/R8t1ULGUU2/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/check.vcf.gz | /<>/bcftools convert -g -,. --chrom .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom /tmp/R8t1ULGUU2/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/check.vcf.gz | /<>/bcftools convert -g .,- --chrom .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/R8t1ULGUU2/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/check.vcf.gz | /<>/bcftools convert -g -,. --chrom --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/R8t1ULGUU2/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/R8t1ULGUU2/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/convert.vcf.gz | /<>/bcftools convert -h -,.,. .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/R8t1ULGUU2/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/convert.vcf.gz | /<>/bcftools convert -h .,-,. .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/R8t1ULGUU2/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/convert.vcf.gz | /<>/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /<>/bcftools convert -H /<>/test/convert.hls.gt.hap,/<>/test/convert.hls.gt.legend,/<>/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /<>/bcftools convert -H /<>/test/convert.hls.gt.hap,/<>/test/convert.hls.gt.legend,/<>/test/convert.hls.gt.samples -Ou | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples -Ou | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/R8t1ULGUU2/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/convert.vcf.gz | /<>/bcftools convert --hapsample -,. .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/R8t1ULGUU2/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/convert.vcf.gz | /<>/bcftools convert --hapsample .,- .. ok test_vcf_convert: /<>/bcftools convert --haplegendsample -,.,. /tmp/R8t1ULGUU2/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/convert.hap-missing.vcf.gz | /<>/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert_gvcf: /<>/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /<>/test/gvcf.fa /tmp/R8t1ULGUU2/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/R8t1ULGUU2/convert.gvcf.vcf.gz | /<>/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /<>/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /<>/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /<>/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.23andme | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/R8t1ULGUU2/consensus.1.chain.new >/dev/null; cat /tmp/R8t1ULGUU2/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/R8t1ULGUU2/consensus.2.chain.new >/dev/null; cat /tmp/R8t1ULGUU2/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab -c /tmp/R8t1ULGUU2/consensus.3.chain.new >/dev/null; cat /tmp/R8t1ULGUU2/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/R8t1ULGUU2/consensus.4.chain.new >/dev/null; cat /tmp/R8t1ULGUU2/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/empty.vcf.gz -f /<>/test/consensus.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus4.vcf.gz -f /<>/test/consensus2.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus5.vcf.gz -f /<>/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus6.vcf.gz -f /<>/test/consensus6.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R8t1ULGUU2/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1pIu .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -b /tmp/R8t1ULGUU2/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/R8t1ULGUU2/mpileup.bam.urllist | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -b /tmp/R8t1ULGUU2/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/R8t1ULGUU2/mpileup.cram.urllist | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa /<>/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa -Ob /<>/test/mpileup/indel-AD.1.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa /<>/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa -Ob /<>/test/mpileup/indel-AD.1.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/SCR,FMT/SCR -f /<>/test/mpileup/mpileup-SCR.fa /<>/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/SCR,FMT/SCR -f /<>/test/mpileup/mpileup-SCR.fa -Ob /<>/test/mpileup/mpileup-SCR.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/SCR,FMT/SCR -f /<>/test/mpileup/mpileup-SCR.fa /<>/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/SCR,FMT/SCR -f /<>/test/mpileup/mpileup-SCR.fa -Ob /<>/test/mpileup/mpileup-SCR.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /<>/bcftools csq -f /<>/test/csq.fa -g /<>/test/csq.gff3 /<>/test/csq.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000318249/ENST00000318249.fa -g /<>/test/csq/ENST00000318249/ENST00000318249.gff /<>/test/csq/ENST00000318249/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000318249/ENST00000318249.fa -g /<>/test/csq/ENST00000318249/ENST00000318249.gff /<>/test/csq/ENST00000318249/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/EDUMMY0002/EDUMMY0002.fa -g /<>/test/csq/EDUMMY0002/EDUMMY0002.gff /<>/test/csq/EDUMMY0002/boundaries.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000295641/ENST00000295641.fa -g /<>/test/csq/ENST00000295641/ENST00000295641.gff /<>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000295641/ENST00000295641.fa -g /<>/test/csq/ENST00000295641/ENST00000295641.gff /<>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000329454/ENST00000329454.fa -g /<>/test/csq/ENST00000329454/ENST00000329454.gff /<>/test/csq/ENST00000329454/boundary-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000329454/ENST00000329454.fa -g /<>/test/csq/ENST00000329454/ENST00000329454.gff /<>/test/csq/ENST00000329454/boundary-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000557788/ENST00000557788.fa -g /<>/test/csq/ENST00000557788/ENST00000557788.gff /<>/test/csq/ENST00000557788/long-overlap-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/snps.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/snps.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/insert3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/insert3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000448695/ENST00000448695.fa -g /<>/test/csq/ENST00000448695/ENST00000448695.gff /<>/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000303039/ENST00000303039.fa -g /<>/test/csq/ENST00000303039/ENST00000303039.gff /<>/test/csq/ENST00000303039/not-a-stop.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000303039/ENST00000303039.fa -g /<>/test/csq/ENST00000303039/ENST00000303039.gff /<>/test/csq/ENST00000303039/not-a-stop.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000520795/ENST00000520795.fa -g /<>/test/csq/ENST00000520795/ENST00000520795.gff /<>/test/csq/ENST00000520795/long-inside-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000520795/ENST00000520795.fa -g /<>/test/csq/ENST00000520795/ENST00000520795.gff /<>/test/csq/ENST00000520795/long-inside-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000256452/ENST00000256452.fa -g /<>/test/csq/ENST00000256452/ENST00000256452.gff /<>/test/csq/ENST00000256452/intron.vcf | /<>/test/csq/sort-csq | /<>/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 /<>/test/csq/ENSMUST00000121418 && /<>/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /<>/test/csq/ENSMUST00000121418 && /<>/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /<>/test/csq/ENSMUST00000121418 && /<>/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000368801/ENST00000368801.fa -g /<>/test/csq/ENST00000368801/ENST00000368801.gff /<>/test/csq/ENST00000368801/compound-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000413103/ENST00000413103.fa -g /<>/test/csq/ENST00000413103/ENST00000413103.gff /<>/test/csq/ENST00000413103/long-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000479739/ENST00000479739.fa -g /<>/test/csq/ENST00000479739/ENST00000479739.gff /<>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000479739/ENST00000479739.fa -g /<>/test/csq/ENST00000479739/ENST00000479739.gff /<>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000518414/ENST00000518414.fa -g /<>/test/csq/ENST00000518414/ENST00000518414.gff /<>/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000400151/ENST00000400151.fa -g /<>/test/csq/ENST00000400151/ENST00000400151.gff /<>/test/csq/ENST00000400151/long-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000390520/ENST00000390520.fa -g /<>/test/csq/ENST00000390520/ENST00000390520.gff /<>/test/csq/ENST00000390520/deletion-overlap.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000382647/ENST00000382647.fa -g /<>/test/csq/ENST00000382647/ENST00000382647.gff /<>/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000378322/ENST00000378322.fa -g /<>/test/csq/ENST00000378322/ENST00000378322.gff /<>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000378322/ENST00000378322.fa -g /<>/test/csq/ENST00000378322/ENST00000378322.gff /<>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000410009/ENST00000410009.fa -g /<>/test/csq/ENST00000410009/ENST00000410009.gff /<>/test/csq/ENST00000410009/frameshift.vcf | /<>/test/csq/sort-csq | /<>/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 /<>/test/csq/ENST00000410009 && /<>/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /<>/test/csq/ENST00000410009 && /<>/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000573314/ENST00000573314.fa -g /<>/test/csq/ENST00000573314/ENST00000573314.gff /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000573314/ENST00000573314.fa -g /<>/test/csq/ENST00000573314/ENST00000573314.gff /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000218032/ENST00000218032.fa -g /<>/test/csq/ENST00000218032/ENST00000218032.gff /<>/test/csq/ENST00000218032/start-lost-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000218032/ENST00000218032.fa -g /<>/test/csq/ENST00000218032/ENST00000218032.gff /<>/test/csq/ENST00000218032/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000218032/ENST00000218032.fa -g /<>/test/csq/ENST00000218032/ENST00000218032.gff /<>/test/csq/ENST00000218032/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /<>/test/csq/ENST00000318249.2/ENST00000318249.2.gff /<>/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000542803/ENST00000542803.fa -g /<>/test/csq/ENST00000542803/ENST00000542803.gff /<>/test/csq/ENST00000542803/splice-region.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000542803/ENST00000542803.fa -g /<>/test/csq/ENST00000542803/ENST00000542803.gff /<>/test/csq/ENST00000542803/splice-region.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000375992/ENST00000375992.fa -g /<>/test/csq/ENST00000375992/ENST00000375992.gff /<>/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000294661/ENST00000294661.fa -g /<>/test/csq/ENST00000294661/ENST00000294661.gff /<>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000294661/ENST00000294661.fa -g /<>/test/csq/ENST00000294661/ENST00000294661.gff /<>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000373833/ENST00000373833.fa -g /<>/test/csq/ENST00000373833/ENST00000373833.gff /<>/test/csq/ENST00000373833/boundary-insertion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000373833/ENST00000373833.fa -g /<>/test/csq/ENST00000373833/ENST00000373833.gff /<>/test/csq/ENST00000373833/boundary-insertion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000357367/ENST00000357367.fa -g /<>/test/csq/ENST00000357367/ENST00000357367.gff /<>/test/csq/ENST00000357367/stop-retained.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000271583/ENST00000271583.fa -g /<>/test/csq/ENST00000271583/ENST00000271583.gff /<>/test/csq/ENST00000271583/splice-acceptor.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /<>/test/csq/ENST00000368801.2/ENST00000368801.2.gff /<>/test/csq/ENST00000368801.2/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000436063/ENST00000436063.fa -g /<>/test/csq/ENST00000436063/ENST00000436063.gff /<>/test/csq/ENST00000436063/insert-before-utr.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000420190/ENST00000420190.fa -g /<>/test/csq/ENST00000420190/ENST00000420190.gff /<>/test/csq/ENST00000420190/abort-in-csq-push.vcf | /<>/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000593942/ENST00000593942.fa -g /<>/test/csq/ENST00000593942/ENST00000593942.gff /<>/test/csq/ENST00000593942/last-codon-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000409523/ENST00000409523.fa -g /<>/test/csq/ENST00000409523/ENST00000409523.gff /<>/test/csq/ENST00000409523/long-overlapping-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000381157/ENST00000381157.fa -g /<>/test/csq/ENST00000381157/ENST00000381157.gff /<>/test/csq/ENST00000381157/haploid-diploid.vcf | /<>/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENSG00000173376/ENSG00000173376.fa -g /<>/test/csq/ENSG00000173376/ENSG00000173376.gff /<>/test/csq/ENSG00000173376/synon.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000545279/ENST00000545279.fa -g /<>/test/csq/ENST00000545279/ENST00000545279.gff /<>/test/csq/ENST00000545279/splice-region-insert.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000536784/ENST00000536784.fa -g /<>/test/csq/ENST00000536784/ENST00000536784.gff /<>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000536784/ENST00000536784.fa -g /<>/test/csq/ENST00000536784/ENST00000536784.gff /<>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /<>/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /<>/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/EDUMMY0003/EDUMMY0003.fa -g /<>/test/csq/EDUMMY0003/EDUMMY0003.gff /<>/test/csq/EDUMMY0003/long-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000420670/ENST00000420670.fa -g /<>/test/csq/ENST00000420670/ENST00000420670.gff /<>/test/csq/ENST00000420670/start-stop-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000420670/ENST00000420670.fa -g /<>/test/csq/ENST00000420670/ENST00000420670.gff /<>/test/csq/ENST00000420670/segfault.vcf | /<>/test/csq/sort-csq | /<>/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 /<>/test/csq/ENSMUST00000133836 && /<>/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000519442/ENST00000519442.fa -g /<>/test/csq/ENST00000519442/ENST00000519442.gff /<>/test/csq/ENST00000519442/synon-splice-region-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000301246/ENST00000301246.fa -g /<>/test/csq/ENST00000301246/ENST00000301246.gff /<>/test/csq/ENST00000301246/15bp-insert.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000520868/ENST00000520868.fa -g /<>/test/csq/ENST00000520868/ENST00000520868.gff /<>/test/csq/ENST00000520868/long-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000528237/ENST00000528237.fa -g /<>/test/csq/ENST00000528237/ENST00000528237.gff /<>/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /<>/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /<>/test/csq/ENST00000263103-INS/insertions.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000624631/ENST00000624631.fa -g /<>/test/csq/ENST00000624631/ENST00000624631.gff /<>/test/csq/ENST00000624631/ambiguous.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000230048/ENST00000230048.fa -g /<>/test/csq/ENST00000230048/ENST00000230048.gff /<>/test/csq/ENST00000230048/start-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000227471/ENST00000227471.fa -g /<>/test/csq/ENST00000227471/ENST00000227471.gff /<>/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000543077/ENST00000543077.fa -g /<>/test/csq/ENST00000543077/ENST00000543077.gff /<>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000543077/ENST00000543077.fa -g /<>/test/csq/ENST00000543077/ENST00000543077.gff /<>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/EDUMMY0001/EDUMMY0001.fa -g /<>/test/csq/EDUMMY0001/EDUMMY0001.gff /<>/test/csq/EDUMMY0001/starts-with-1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/EDUMMY0001/EDUMMY0001.fa -g /<>/test/csq/EDUMMY0001/EDUMMY0001.gff /<>/test/csq/EDUMMY0001/starts-with-1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok Number of tests: total .. 961 passed .. 961 failed .. 0 make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_auto_install -a make -j4 install DESTDIR=/<>/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' mkdir -p -m 755 /<>/debian/bcftools/usr/bin /<>/debian/bcftools/usr/share/man/man1 /<>/debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools install -p bcftools /<>/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /<>/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /<>/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /<>/debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/<>' dh_installman --language=C make[1]: Leaving directory '/<>' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing bcftools (in debian/bcftools); do_strip: , oemstrip: pkgstriptranslations: processing bcftools-dbgsym (in debian/.debhelper/bcftools/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/bcftools/DEBIAN/control, package bcftools, directory debian/bcftools pkgstripfiles: Truncating usr/share/doc/bcftools/changelog.Debian.gz to topmost ten records pkgstripfiles: processing control file: debian/.debhelper/bcftools/dbgsym-root/DEBIAN/control, package bcftools-dbgsym, directory debian/.debhelper/bcftools/dbgsym-root dpkg-deb: building package 'bcftools-dbgsym' in 'debian/.debhelper/scratch-space/build-bcftools/bcftools-dbgsym_1.10.2-4_arm64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package bcftools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'bcftools' in '../bcftools_1.10.2-4_arm64.deb'. Renaming bcftools-dbgsym_1.10.2-4_arm64.deb to bcftools-dbgsym_1.10.2-4_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../bcftools_1.10.2-4_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20200715-0517 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bcftools_1.10.2-4_arm64.changes: -------------------------------- Format: 1.8 Date: Tue, 14 Jul 2020 22:39:24 +0200 Source: bcftools Binary: bcftools Architecture: arm64 Version: 1.10.2-4 Distribution: groovy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Closes: 965032 Changes: bcftools (1.10.2-4) unstable; urgency=medium . * Fix suggested Python packages Closes: #965032 Checksums-Sha1: e4e05b61ceee30a17d435cc8091005677a45ef7d 1620552 bcftools-dbgsym_1.10.2-4_arm64.ddeb edc07e7450849598ec81739b45bb2588ed73deca 6560 bcftools_1.10.2-4_arm64.buildinfo 3a542e903b28b46d37277895b1f0bfc77797aa54 545616 bcftools_1.10.2-4_arm64.deb Checksums-Sha256: 6118dcbedf0541d02a7afad75892d8ad876413405d6dd4eb2bf6a27ab1db2bb2 1620552 bcftools-dbgsym_1.10.2-4_arm64.ddeb 710d16f92c97d8a30f3aa4deaaccefd7be9d4f43099c8e66c5d7b6e7231bacb1 6560 bcftools_1.10.2-4_arm64.buildinfo b4c2f91358e16de9d76b701d871363f8c7c09abc7bd06157fbca0da7291274ad 545616 bcftools_1.10.2-4_arm64.deb Files: e14aa49a8d8b4123cc326009c0273788 1620552 debug optional bcftools-dbgsym_1.10.2-4_arm64.ddeb 35e26cb59b643d58fad5fd36db3b967d 6560 science optional bcftools_1.10.2-4_arm64.buildinfo a292d9783d72b6e64aa54f4dced3e948 545616 science optional bcftools_1.10.2-4_arm64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bcftools_1.10.2-4_arm64.deb --------------------------- new debian package, version 2.0. size 545616 bytes: control archive=2216 bytes. 835 bytes, 18 lines control 3927 bytes, 51 lines md5sums Package: bcftools Version: 1.10.2-4 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1901 Depends: libc6 (>= 2.29), libhts3 (>= 1.10), zlib1g (>= 1:1.1.4) Recommends: perl Suggests: python3, python3-numpy, python3-matplotlib, texlive-latex-recommended Breaks: samtools (<< 1.0) Replaces: samtools (<< 1.0) Section: science Priority: optional Homepage: http://samtools.github.io/bcftools/ Description: genomic variant calling and manipulation of VCF/BCF files BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. drwxr-xr-x root/root 0 2020-07-14 20:39 ./ drwxr-xr-x root/root 0 2020-07-14 20:39 ./usr/ drwxr-xr-x root/root 0 2020-07-14 20:39 ./usr/bin/ -rwxr-xr-x root/root 920480 2020-07-14 20:39 ./usr/bin/bcftools -rwxr-xr-x root/root 16943 2020-07-14 20:39 ./usr/bin/color-chrs.pl -rwxr-xr-x root/root 4320 2020-07-14 20:39 ./usr/bin/guess-ploidy.py -rwxr-xr-x root/root 15158 2020-07-14 20:39 ./usr/bin/plot-roh.py -rwxr-xr-x root/root 79901 2020-07-14 20:39 ./usr/bin/plot-vcfstats -rwxr-xr-x root/root 13371 2020-07-14 20:39 ./usr/bin/run-roh.pl -rwxr-xr-x root/root 18196 2020-07-14 20:39 ./usr/bin/vcfutils.pl drwxr-xr-x root/root 0 2020-07-14 20:39 ./usr/lib/ drwxr-xr-x root/root 0 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/ drwxr-xr-x root/root 0 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/ -rw-r--r-- root/root 18776 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/GTisec.so -rw-r--r-- root/root 10488 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/GTsubset.so -rw-r--r-- root/root 72288 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/ad-bias.so -rw-r--r-- root/root 14456 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/add-variantkey.so -rw-r--r-- root/root 14696 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/af-dist.so -rw-r--r-- root/root 10336 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/allele-length.so -rw-r--r-- root/root 10360 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/check-ploidy.so -rw-r--r-- root/root 14816 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/check-sparsity.so -rw-r--r-- root/root 22872 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/color-chrs.so -rw-r--r-- root/root 23416 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/contrast.so -rw-r--r-- root/root 10328 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/counts.so -rw-r--r-- root/root 18672 2020-07-14 20:39 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-rw-r--r-- root/root 14816 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/isecGT.so -rw-r--r-- root/root 23288 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/mendelian.so -rw-r--r-- root/root 10472 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/missing2ref.so -rw-r--r-- root/root 19008 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/parental-origin.so -rw-r--r-- root/root 19232 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/prune.so -rw-r--r-- root/root 14944 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/remove-overlaps.so -rw-r--r-- root/root 18816 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/setGT.so -rw-r--r-- root/root 19008 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/smpl-stats.so -rw-r--r-- root/root 35960 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/split-vep.so -rw-r--r-- root/root 23216 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/split.so -rw-r--r-- root/root 14728 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/tag2tag.so -rw-r--r-- root/root 19192 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/trio-dnm.so -rw-r--r-- root/root 23304 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/trio-stats.so -rw-r--r-- root/root 14624 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/trio-switch-rate.so -rw-r--r-- root/root 14504 2020-07-14 20:39 ./usr/lib/aarch64-linux-gnu/bcftools/variantkey-hex.so drwxr-xr-x root/root 0 2020-07-14 20:39 ./usr/share/ drwxr-xr-x root/root 0 2020-07-14 20:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-07-14 20:39 ./usr/share/doc/bcftools/ -rw-r--r-- root/root 246 2019-12-19 09:57 ./usr/share/doc/bcftools/README -rw-r--r-- root/root 966 2020-07-14 20:39 ./usr/share/doc/bcftools/changelog.Debian.gz -rw-r--r-- root/root 2550 2020-07-14 20:39 ./usr/share/doc/bcftools/copyright drwxr-xr-x root/root 0 2020-07-14 20:39 ./usr/share/man/ drwxr-xr-x root/root 0 2020-07-14 20:39 ./usr/share/man/man1/ -rw-r--r-- root/root 36625 2020-07-14 20:39 ./usr/share/man/man1/bcftools.1.gz -rw-r--r-- root/root 253 2020-07-14 20:39 ./usr/share/man/man1/color-chrs.pl.1.gz -rw-r--r-- root/root 271 2020-07-14 20:39 ./usr/share/man/man1/plot-vcfstats.1.gz -rw-r--r-- root/root 208 2020-07-14 20:39 ./usr/share/man/man1/vcfutils.pl.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 40100 Build-Time: 160 Distribution: groovy-proposed Host Architecture: arm64 Install-Time: 25 Job: bcftools_1.10.2-4.dsc Machine Architecture: arm64 Package: bcftools Package-Time: 187 Source-Version: 1.10.2-4 Space: 40100 Status: successful Version: 1.10.2-4 -------------------------------------------------------------------------------- Finished at 20200715-0517 Build needed 00:03:07, 40100k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-19591624 Scanning for processes to kill in build PACKAGEBUILD-19591624