https://launchpad.net/ubuntu/+archive/test-rebuild-20210927-impish/+build/22121190 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-010 4.15.0-159-generic #167-Ubuntu SMP Mon Sep 20 23:06:52 UTC 2021 aarch64 Buildd toolchain package versions: launchpad-buildd_202~502~ubuntu18.04.1 python3-lpbuildd_202~502~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.9 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 5 Oct 21:53:45 ntpdate[1694]: adjust time server 10.211.37.1 offset 0.007376 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=impish --arch=armhf PACKAGEBUILD-22121190 --image-type chroot /home/buildd/filecache-default/97616dc8f1f80df2f95e447b7ddaa1d0ac1b5f62 Creating target for build PACKAGEBUILD-22121190 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=impish --arch=armhf PACKAGEBUILD-22121190 Starting target for build PACKAGEBUILD-22121190 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=impish --arch=armhf PACKAGEBUILD-22121190 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish main' 'deb http://ftpmaster.internal/ubuntu impish main universe' Overriding sources.list in build-PACKAGEBUILD-22121190 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=impish --arch=armhf PACKAGEBUILD-22121190 Adding trusted keys to build-PACKAGEBUILD-22121190 Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). OK Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=impish --arch=armhf PACKAGEBUILD-22121190 Updating target for build PACKAGEBUILD-22121190 Get:1 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish InRelease [17.5 kB] Get:2 http://ftpmaster.internal/ubuntu impish InRelease [269 kB] Get:3 http://ftpmaster.internal/ubuntu impish/main armhf Packages [1358 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main armhf Packages [10.7 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main Translation-en [10.5 kB] Get:6 http://ftpmaster.internal/ubuntu impish/main Translation-en [514 kB] Get:7 http://ftpmaster.internal/ubuntu impish/universe armhf Packages [12.6 MB] Get:8 http://ftpmaster.internal/ubuntu impish/universe Translation-en [5461 kB] Fetched 20.2 MB in 5s (4126 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: g++-10 libstdc++-10-dev Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libffi8ubuntu1* The following NEW packages will be installed: cpp-11 g++-11 gcc-11 libexpat1 libffi8 libgcc-11-dev libmpdec3 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libstdc++-11-dev media-types python3 python3-minimal python3-psutil python3.9 python3.9-minimal The following packages will be upgraded: advancecomp apt base-files base-passwd bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils build-essential ca-certificates cpp cpp-10 dash debconf diffutils dpkg dpkg-dev e2fsprogs findutils g++ g++-10 gcc gcc-10 gcc-10-base gcc-11-base gpg gpg-agent gpgconf gpgv grep gzip libapparmor1 libapt-pkg6.0 libasan6 libassuan0 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdevmapper1.02.1 libdpkg-perl libext2fs2 libgcc-10-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgssapi-krb5-2 libhogweed6 libidn2-0 libisl23 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblz4-1 liblzma5 libmount1 libnettle8 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.32 libprocps8 libreadline8 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-10-dev libstdc++6 libsystemd0 libtirpc-common libtirpc-dev libtirpc3 libubsan1 libudev1 libunistring2 libuuid1 libzstd1 linux-libc-dev login logsave lto-disabled-list mount openssl passwd perl perl-base perl-modules-5.32 pinentry-curses pkgbinarymangler procps readline-common systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata usrmerge util-linux xz-utils zlib1g 122 upgraded, 17 newly installed, 1 to remove and 0 not upgraded. Need to get 245 MB of archives. After this operation, 453 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu impish/main armhf libcrypt-dev armhf 1:4.4.18-4ubuntu1 [112 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main armhf dpkg armhf 1.20.9ubuntu13 [1215 kB] Get:3 http://ftpmaster.internal/ubuntu impish/main armhf libnsl-dev armhf 1.3.0-2 [61.2 kB] Get:4 http://ftpmaster.internal/ubuntu impish/main armhf libc6-dev armhf 2.34-0ubuntu2 [1314 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main armhf g++ armhf 4:11.2.0-1ubuntu1 [1400 B] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main armhf gcc armhf 4:11.2.0-1ubuntu1 [5126 B] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main armhf cpp armhf 4:11.2.0-1ubuntu1 [27.7 kB] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main armhf dpkg-dev all 1.20.9ubuntu13 [938 kB] Get:9 http://ftpmaster.internal/ubuntu impish/main armhf libc-dev-bin armhf 2.34-0ubuntu2 [18.9 kB] Get:10 http://ftpmaster.internal/ubuntu impish/main armhf libcrypt1 armhf 1:4.4.18-4ubuntu1 [86.6 kB] Get:11 http://ftpmaster.internal/ubuntu impish/main armhf libtirpc-common all 1.3.2-2 [7674 B] Get:12 http://ftpmaster.internal/ubuntu impish/main armhf libtirpc-dev armhf 1.3.2-2 [184 kB] Get:13 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main armhf libdpkg-perl all 1.20.9ubuntu13 [235 kB] Get:14 http://ftpmaster.internal/ubuntu impish/main armhf libk5crypto3 armhf 1.18.3-6 [83.9 kB] Get:15 http://ftpmaster.internal/ubuntu impish/main armhf libkrb5support0 armhf 1.18.3-6 [30.2 kB] Get:16 http://ftpmaster.internal/ubuntu impish/main armhf libkrb5-3 armhf 1.18.3-6 [330 kB] Get:17 http://ftpmaster.internal/ubuntu impish/main armhf libgssapi-krb5-2 armhf 1.18.3-6 [120 kB] Get:18 http://ftpmaster.internal/ubuntu impish/main armhf libcom-err2 armhf 1.46.3-1ubuntu3 [9852 B] Get:19 http://ftpmaster.internal/ubuntu impish/main armhf libperl5.32 armhf 5.32.1-3ubuntu3 [3985 kB] Get:20 http://ftpmaster.internal/ubuntu impish/main armhf perl armhf 5.32.1-3ubuntu3 [227 kB] Get:21 http://ftpmaster.internal/ubuntu impish/main armhf perl-base armhf 5.32.1-3ubuntu3 [1598 kB] Get:22 http://ftpmaster.internal/ubuntu impish/main armhf perl-modules-5.32 all 5.32.1-3ubuntu3 [2945 kB] Get:23 http://ftpmaster.internal/ubuntu impish/main armhf libdb5.3 armhf 5.3.28+dfsg1-0.8ubuntu1 [585 kB] Get:24 http://ftpmaster.internal/ubuntu impish/main armhf zlib1g armhf 1:1.2.11.dfsg-2ubuntu7 [51.3 kB] Get:25 http://ftpmaster.internal/ubuntu impish/main armhf debconf all 1.5.77 [121 kB] Get:26 http://ftpmaster.internal/ubuntu impish/main armhf libc6 armhf 2.34-0ubuntu2 [2500 kB] Get:27 http://ftpmaster.internal/ubuntu impish/main armhf libc-bin armhf 2.34-0ubuntu2 [843 kB] Get:28 http://ftpmaster.internal/ubuntu impish/main armhf libssl1.1 armhf 1.1.1l-1ubuntu1 [1200 kB] Get:29 http://ftpmaster.internal/ubuntu impish/main armhf libtirpc3 armhf 1.3.2-2 [72.3 kB] Get:30 http://ftpmaster.internal/ubuntu impish/main armhf libnsl2 armhf 1.3.0-2 [33.3 kB] Get:31 http://ftpmaster.internal/ubuntu impish/main armhf linux-libc-dev armhf 5.13.0-16.16 [1240 kB] Get:32 http://ftpmaster.internal/ubuntu impish/main armhf libasan6 armhf 11.2.0-7ubuntu2 [2242 kB] Get:33 http://ftpmaster.internal/ubuntu impish/main armhf libubsan1 armhf 11.2.0-7ubuntu2 [893 kB] Get:34 http://ftpmaster.internal/ubuntu impish/main armhf libgomp1 armhf 11.2.0-7ubuntu2 [100 kB] Get:35 http://ftpmaster.internal/ubuntu impish/main armhf gcc-11-base armhf 11.2.0-7ubuntu2 [20.6 kB] Get:36 http://ftpmaster.internal/ubuntu impish/main armhf libgcc-s1 armhf 11.2.0-7ubuntu2 [42.6 kB] Get:37 http://ftpmaster.internal/ubuntu impish/main armhf libcc1-0 armhf 11.2.0-7ubuntu2 [45.8 kB] Get:38 http://ftpmaster.internal/ubuntu impish/main armhf libatomic1 armhf 11.2.0-7ubuntu2 [7626 B] Get:39 http://ftpmaster.internal/ubuntu impish/main armhf libstdc++6 armhf 11.2.0-7ubuntu2 [572 kB] Get:40 http://ftpmaster.internal/ubuntu impish/main armhf base-files armhf 11.1ubuntu3 [60.6 kB] Get:41 http://ftpmaster.internal/ubuntu impish/main armhf bash armhf 5.1-3ubuntu1 [605 kB] Get:42 http://ftpmaster.internal/ubuntu impish/main armhf bsdutils armhf 1:2.36.1-8ubuntu1 [86.7 kB] Get:43 http://ftpmaster.internal/ubuntu impish/main armhf dash armhf 0.5.11+git20210120+802ebd4-1 [78.7 kB] Get:44 http://ftpmaster.internal/ubuntu impish/main armhf diffutils armhf 1:3.8-0ubuntu1 [192 kB] Get:45 http://ftpmaster.internal/ubuntu impish/main armhf findutils armhf 4.8.0-1ubuntu2 [323 kB] Get:46 http://ftpmaster.internal/ubuntu impish/main armhf grep armhf 3.7-0ubuntu1 [185 kB] Get:47 http://ftpmaster.internal/ubuntu impish/main armhf gzip armhf 1.10-4ubuntu1 [91.1 kB] Get:48 http://ftpmaster.internal/ubuntu impish/main armhf login armhf 1:4.8.1-1ubuntu9 [221 kB] Get:49 http://ftpmaster.internal/ubuntu impish/main armhf util-linux armhf 2.36.1-8ubuntu1 [1072 kB] Get:50 http://ftpmaster.internal/ubuntu impish/main armhf base-passwd armhf 3.5.51 [48.6 kB] Get:51 http://ftpmaster.internal/ubuntu impish/main armhf sysvinit-utils armhf 2.96-7ubuntu1 [19.2 kB] Get:52 http://ftpmaster.internal/ubuntu impish/main armhf libgcrypt20 armhf 1.8.7-5ubuntu2 [408 kB] Get:53 http://ftpmaster.internal/ubuntu impish/main armhf liblz4-1 armhf 1.9.3-2 [49.6 kB] Get:54 http://ftpmaster.internal/ubuntu impish/main armhf liblzma5 armhf 5.2.5-2 [83.7 kB] Get:55 http://ftpmaster.internal/ubuntu impish/main armhf systemd-sysv armhf 248.3-1ubuntu7 [10.5 kB] Get:56 http://ftpmaster.internal/ubuntu impish/main armhf systemd-timesyncd armhf 248.3-1ubuntu7 [30.6 kB] Get:57 http://ftpmaster.internal/ubuntu impish/main armhf libapparmor1 armhf 3.0.3-0ubuntu1 [32.7 kB] Get:58 http://ftpmaster.internal/ubuntu impish/main armhf libaudit-common all 1:3.0-2ubuntu2 [4788 B] Get:59 http://ftpmaster.internal/ubuntu impish/main armhf libaudit1 armhf 1:3.0-2ubuntu2 [37.1 kB] Get:60 http://ftpmaster.internal/ubuntu impish/main armhf libblkid1 armhf 2.36.1-8ubuntu1 [131 kB] Get:61 http://ftpmaster.internal/ubuntu impish/main armhf libudev1 armhf 248.3-1ubuntu7 [69.1 kB] Get:62 http://ftpmaster.internal/ubuntu impish/main armhf libdevmapper1.02.1 armhf 2:1.02.175-2.1ubuntu1 [120 kB] Get:63 http://ftpmaster.internal/ubuntu impish/main armhf libuuid1 armhf 2.36.1-8ubuntu1 [22.7 kB] Get:64 http://ftpmaster.internal/ubuntu impish/main armhf libcryptsetup12 armhf 2:2.3.6-0ubuntu1 [193 kB] Get:65 http://ftpmaster.internal/ubuntu impish/main armhf libnettle8 armhf 3.7.3-1 [159 kB] Get:66 http://ftpmaster.internal/ubuntu impish/main armhf libhogweed6 armhf 3.7.3-1 [183 kB] Get:67 http://ftpmaster.internal/ubuntu impish/main armhf libunistring2 armhf 0.9.10-6 [478 kB] Get:68 http://ftpmaster.internal/ubuntu impish/main armhf libidn2-0 armhf 2.3.1-1 [50.3 kB] Get:69 http://ftpmaster.internal/ubuntu impish/main armhf libffi8 armhf 3.4.2-1ubuntu5 [17.8 kB] Get:70 http://ftpmaster.internal/ubuntu impish/main armhf libp11-kit0 armhf 0.23.22-1build1 [217 kB] Get:71 http://ftpmaster.internal/ubuntu impish/main armhf libgnutls30 armhf 3.7.1-5ubuntu1 [921 kB] Get:72 http://ftpmaster.internal/ubuntu impish/main armhf libzstd1 armhf 1.4.8+dfsg-2.1 [255 kB] Get:73 http://ftpmaster.internal/ubuntu impish/main armhf libkmod2 armhf 28-1ubuntu4 [37.8 kB] Get:74 http://ftpmaster.internal/ubuntu impish/main armhf libmount1 armhf 2.36.1-8ubuntu1 [146 kB] Get:75 http://ftpmaster.internal/ubuntu impish/main armhf libpam0g armhf 1.3.1-5ubuntu11 [53.1 kB] Get:76 http://ftpmaster.internal/ubuntu impish/main armhf mount armhf 2.36.1-8ubuntu1 [122 kB] Get:77 http://ftpmaster.internal/ubuntu impish/main armhf systemd armhf 248.3-1ubuntu7 [4305 kB] Get:78 http://ftpmaster.internal/ubuntu impish/main armhf libsystemd0 armhf 248.3-1ubuntu7 [285 kB] Get:79 http://ftpmaster.internal/ubuntu impish/main armhf libapt-pkg6.0 armhf 2.3.9 [895 kB] Get:80 http://ftpmaster.internal/ubuntu impish/main armhf gpgv armhf 2.2.20-1ubuntu4 [172 kB] Get:81 http://ftpmaster.internal/ubuntu impish/main armhf apt armhf 2.3.9 [1373 kB] Get:82 http://ftpmaster.internal/ubuntu impish/main armhf libpam-modules-bin armhf 1.3.1-5ubuntu11 [40.2 kB] Get:83 http://ftpmaster.internal/ubuntu impish/main armhf libpam-modules armhf 1.3.1-5ubuntu11 [255 kB] Get:84 http://ftpmaster.internal/ubuntu impish/main armhf logsave armhf 1.46.3-1ubuntu3 [10.9 kB] Get:85 http://ftpmaster.internal/ubuntu impish/main armhf libext2fs2 armhf 1.46.3-1ubuntu3 [192 kB] Get:86 http://ftpmaster.internal/ubuntu impish/main armhf e2fsprogs armhf 1.46.3-1ubuntu3 [562 kB] Get:87 http://ftpmaster.internal/ubuntu impish/main armhf libpython3.9-minimal armhf 3.9.7-2build1 [772 kB] Get:88 http://ftpmaster.internal/ubuntu impish/main armhf libexpat1 armhf 2.4.1-2 [64.8 kB] Get:89 http://ftpmaster.internal/ubuntu impish/main armhf python3.9-minimal armhf 3.9.7-2build1 [1751 kB] Get:90 http://ftpmaster.internal/ubuntu impish/main armhf python3-minimal armhf 3.9.4-1 [23.8 kB] Get:91 http://ftpmaster.internal/ubuntu impish/main armhf media-types all 4.0.0 [22.2 kB] Get:92 http://ftpmaster.internal/ubuntu impish/main armhf tzdata all 2021a-2ubuntu1 [339 kB] Get:93 http://ftpmaster.internal/ubuntu impish/main armhf libmpdec3 armhf 2.5.1-2 [69.4 kB] Get:94 http://ftpmaster.internal/ubuntu impish/main armhf readline-common all 8.1-2 [54.1 kB] Get:95 http://ftpmaster.internal/ubuntu impish/main armhf libreadline8 armhf 8.1-2 [114 kB] Get:96 http://ftpmaster.internal/ubuntu impish/main armhf libsqlite3-0 armhf 3.35.5-1 [512 kB] Get:97 http://ftpmaster.internal/ubuntu impish/main armhf libpython3.9-stdlib armhf 3.9.7-2build1 [1731 kB] Get:98 http://ftpmaster.internal/ubuntu impish/main armhf python3.9 armhf 3.9.7-2build1 [433 kB] Get:99 http://ftpmaster.internal/ubuntu impish/main armhf libpython3-stdlib armhf 3.9.4-1 [6984 B] Get:100 http://ftpmaster.internal/ubuntu impish/main armhf python3 armhf 3.9.4-1 [22.2 kB] Get:101 http://ftpmaster.internal/ubuntu impish/main armhf libpam-runtime all 1.3.1-5ubuntu11 [38.7 kB] Get:102 http://ftpmaster.internal/ubuntu impish/main armhf libpcre2-8-0 armhf 10.37-0ubuntu2 [189 kB] Get:103 http://ftpmaster.internal/ubuntu impish/main armhf libsmartcols1 armhf 2.36.1-8ubuntu1 [91.1 kB] Get:104 http://ftpmaster.internal/ubuntu impish/main armhf passwd armhf 1:4.8.1-1ubuntu9 [787 kB] Get:105 http://ftpmaster.internal/ubuntu impish/main armhf libprocps8 armhf 2:3.3.17-5ubuntu3 [32.6 kB] Get:106 http://ftpmaster.internal/ubuntu impish/main armhf libss2 armhf 1.46.3-1ubuntu3 [10.1 kB] Get:107 http://ftpmaster.internal/ubuntu impish/main armhf procps armhf 2:3.3.17-5ubuntu3 [373 kB] Get:108 http://ftpmaster.internal/ubuntu impish/main armhf usrmerge all 25ubuntu1 [53.5 kB] Get:109 http://ftpmaster.internal/ubuntu impish/main armhf openssl armhf 1.1.1l-1ubuntu1 [624 kB] Get:110 http://ftpmaster.internal/ubuntu impish/main armhf ca-certificates all 20210119ubuntu1 [149 kB] Get:111 http://ftpmaster.internal/ubuntu impish/main armhf xz-utils armhf 5.2.5-2 [80.7 kB] Get:112 http://ftpmaster.internal/ubuntu impish/main armhf advancecomp armhf 2.1-2.1ubuntu1 [185 kB] Get:113 http://ftpmaster.internal/ubuntu impish/main armhf libctf0 armhf 2.37-7ubuntu1 [93.8 kB] Get:114 http://ftpmaster.internal/ubuntu impish/main armhf libctf-nobfd0 armhf 2.37-7ubuntu1 [93.6 kB] Get:115 http://ftpmaster.internal/ubuntu impish/main armhf binutils-arm-linux-gnueabihf armhf 2.37-7ubuntu1 [3062 kB] Get:116 http://ftpmaster.internal/ubuntu impish/main armhf libbinutils armhf 2.37-7ubuntu1 [492 kB] Get:117 http://ftpmaster.internal/ubuntu impish/main armhf binutils armhf 2.37-7ubuntu1 [3166 B] Get:118 http://ftpmaster.internal/ubuntu impish/main armhf binutils-common armhf 2.37-7ubuntu1 [212 kB] Get:119 http://ftpmaster.internal/ubuntu impish/main armhf libisl23 armhf 0.24-1 [517 kB] Get:120 http://ftpmaster.internal/ubuntu impish/main armhf cpp-11 armhf 11.2.0-7ubuntu2 [48.0 MB] Get:121 http://ftpmaster.internal/ubuntu impish/main armhf libgcc-11-dev armhf 11.2.0-7ubuntu2 [838 kB] Get:122 http://ftpmaster.internal/ubuntu impish/main armhf gcc-11 armhf 11.2.0-7ubuntu2 [54.8 MB] Get:123 http://ftpmaster.internal/ubuntu impish/main armhf libstdc++-11-dev armhf 11.2.0-7ubuntu2 [2125 kB] Get:124 http://ftpmaster.internal/ubuntu impish/main armhf g++-11 armhf 11.2.0-7ubuntu2 [52.3 MB] Get:125 http://ftpmaster.internal/ubuntu impish/main armhf lto-disabled-list all 16 [12.5 kB] Get:126 http://ftpmaster.internal/ubuntu impish/main armhf python3-psutil armhf 5.8.0-1 [151 kB] Get:127 http://ftpmaster.internal/ubuntu impish/main armhf build-essential armhf 12.9ubuntu1 [4740 B] Get:128 http://ftpmaster.internal/ubuntu impish/universe armhf g++-10 armhf 10.3.0-11ubuntu1 [8460 kB] Get:129 http://ftpmaster.internal/ubuntu impish/universe armhf gcc-10 armhf 10.3.0-11ubuntu1 [15.1 MB] Get:130 http://ftpmaster.internal/ubuntu impish/main armhf libstdc++-10-dev armhf 10.3.0-11ubuntu1 [1961 kB] Get:131 http://ftpmaster.internal/ubuntu impish/main armhf libgcc-10-dev armhf 10.3.0-11ubuntu1 [812 kB] Get:132 http://ftpmaster.internal/ubuntu impish/universe armhf cpp-10 armhf 10.3.0-11ubuntu1 [7427 kB] Get:133 http://ftpmaster.internal/ubuntu impish/main armhf gcc-10-base armhf 10.3.0-11ubuntu1 [20.7 kB] Get:134 http://ftpmaster.internal/ubuntu impish/main armhf libassuan0 armhf 2.5.5-1 [31.4 kB] Get:135 http://ftpmaster.internal/ubuntu impish/main armhf pinentry-curses armhf 1.1.1-1 [32.9 kB] Get:136 http://ftpmaster.internal/ubuntu impish/main armhf gpg armhf 2.2.20-1ubuntu4 [428 kB] Get:137 http://ftpmaster.internal/ubuntu impish/main armhf gpgconf armhf 2.2.20-1ubuntu4 [108 kB] Get:138 http://ftpmaster.internal/ubuntu impish/main armhf gpg-agent armhf 2.2.20-1ubuntu4 [196 kB] Get:139 http://ftpmaster.internal/ubuntu impish/main armhf pkgbinarymangler all 148 [32.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 245 MB in 6s (43.7 MB/s) (Reading database ... 12870 files and directories currently installed.) 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Setting up binutils-common:armhf (2.37-7ubuntu1) ... Setting up linux-libc-dev:armhf (5.13.0-16.16) ... Setting up libctf-nobfd0:armhf (2.37-7ubuntu1) ... Setting up libassuan0:armhf (2.5.5-1) ... Setting up libgomp1:armhf (11.2.0-7ubuntu2) ... Setting up libasan6:armhf (11.2.0-7ubuntu2) ... Setting up tzdata (2021a-2ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Oct 5 21:54:38 UTC 2021. Universal Time is now: Tue Oct 5 21:54:38 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up gcc-10-base:armhf (10.3.0-11ubuntu1) ... Setting up libtirpc-dev:armhf (1.3.2-2) ... Setting up xz-utils (5.2.5-2) ... Setting up libatomic1:armhf (11.2.0-7ubuntu2) ... Setting up usrmerge (25ubuntu1) ... Setting up libss2:armhf (1.46.3-1ubuntu3) ... Setting up libperl5.32:armhf (5.32.1-3ubuntu3) ... Setting up logsave (1.46.3-1ubuntu3) ... Setting up libubsan1:armhf (11.2.0-7ubuntu2) ... Setting up advancecomp (2.1-2.1ubuntu1) ... Setting up libdevmapper1.02.1:armhf (2:1.02.175-2.1ubuntu1) ... Setting up libgcc-11-dev:armhf (11.2.0-7ubuntu2) ... Setting up mount (2.36.1-8ubuntu1) ... Setting up libnsl-dev:armhf (1.3.0-2) ... Setting up libcrypt-dev:armhf (1:4.4.18-4ubuntu1) ... Setting up libmpdec3:armhf (2.5.1-2) ... Setting up libcryptsetup12:armhf (2:2.3.6-0ubuntu1) ... Setting up libbinutils:armhf (2.37-7ubuntu1) ... Setting up libisl23:armhf (0.24-1) ... Setting up libc-dev-bin (2.34-0ubuntu2) ... Setting up openssl (1.1.1l-1ubuntu1) ... Setting up readline-common (8.1-2) ... Setting up libcc1-0:armhf (11.2.0-7ubuntu2) ... Setting up libprocps8:armhf (2:3.3.17-5ubuntu3) ... Setting up cpp-10 (10.3.0-11ubuntu1) ... Setting up libkmod2:armhf (28-1ubuntu4) ... Setting up libctf0:armhf (2.37-7ubuntu1) ... Setting up pinentry-curses (1.1.1-1) ... Setting up cpp-11 (11.2.0-7ubuntu2) ... Setting up pkgbinarymangler (148) ... Setting up libgcc-10-dev:armhf (10.3.0-11ubuntu1) ... Setting up libreadline8:armhf (8.1-2) ... Setting up e2fsprogs (1.46.3-1ubuntu3) ... Setting up ca-certificates (20210119ubuntu1) ... Updating certificates in /etc/ssl/certs... 0 added, 1 removed; done. Setting up perl (5.32.1-3ubuntu3) ... Setting up libdpkg-perl (1.20.9ubuntu13) ... Setting up cpp (4:11.2.0-1ubuntu1) ... Setting up procps (2:3.3.17-5ubuntu3) ... update-alternatives: warning: alternative /usr/bin/w.procps (part of link group w) doesn't exist; removing from list of alternatives update-alternatives: warning: /etc/alternatives/w is dangling; it will be updated with best choice Setting up gpgconf (2.2.20-1ubuntu4) ... Setting up libc6-dev:armhf (2.34-0ubuntu2) ... Setting up binutils-arm-linux-gnueabihf (2.37-7ubuntu1) ... Setting up gpg (2.2.20-1ubuntu4) ... Setting up libpython3.9-stdlib:armhf (3.9.7-2build1) ... Setting up libpython3-stdlib:armhf (3.9.4-1) ... Setting up libstdc++-10-dev:armhf (10.3.0-11ubuntu1) ... Setting up gpg-agent (2.2.20-1ubuntu4) ... Setting up binutils (2.37-7ubuntu1) ... Setting up gcc-10 (10.3.0-11ubuntu1) ... Setting up libstdc++-11-dev:armhf (11.2.0-7ubuntu2) ... Setting up gcc-11 (11.2.0-7ubuntu2) ... Setting up python3.9 (3.9.7-2build1) ... Setting up g++-10 (10.3.0-11ubuntu1) ... Setting up g++-11 (11.2.0-7ubuntu2) ... Setting up python3 (3.9.4-1) ... Setting up python3-psutil (5.8.0-1) ... Setting up gcc (4:11.2.0-1ubuntu1) ... Setting up dpkg-dev (1.20.9ubuntu13) ... Setting up g++ (4:11.2.0-1ubuntu1) ... Setting up build-essential (12.9ubuntu1) ... Setting up systemd-timesyncd (248.3-1ubuntu7) ... Installing new version of config file /etc/systemd/timesyncd.conf ... Setting up systemd (248.3-1ubuntu7) ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/pstore.conf ... Installing new version of config file /etc/systemd/resolved.conf ... Installing new version of config file /etc/systemd/sleep.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up systemd-sysv (248.3-1ubuntu7) ... Processing triggers for libc-bin (2.34-0ubuntu2) ... Processing triggers for ca-certificates (20210119ubuntu1) ... 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-22121190 armhf impish -c chroot:build-PACKAGEBUILD-22121190 --arch=armhf --dist=impish --nolog bcftools_1.11-1.dsc Initiating build PACKAGEBUILD-22121190 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-159-generic #167-Ubuntu SMP Mon Sep 20 23:06:52 UTC 2021 armv7l sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-010.buildd +==============================================================================+ | bcftools 1.11-1 (armhf) Tue, 05 Oct 2021 21:54:50 +0000 | +==============================================================================+ Package: bcftools Version: 1.11-1 Source Version: 1.11-1 Distribution: impish Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22121190/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bcftools_1.11-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/bcftools-gsHQ4P/bcftools-1.11' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-gsHQ4P' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-fbJ6UL/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-fbJ6UL/apt_archive ./ InRelease Get:2 copy:/<>/resolver-fbJ6UL/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-fbJ6UL/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-fbJ6UL/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-fbJ6UL/apt_archive ./ Packages [432 B] Fetched 1738 B in 0s (59.9 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: cpp-10 g++-10 gcc-10 gcc-10-base libgcc-10-dev libstdc++-10-dev 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 652 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-fbJ6UL/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [652 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 652 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14697 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.11), libgsl-dev, tabix, libio-pty-perl Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.11), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<>/resolver-fbJ6UL/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-bcftools-dummy sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-fbJ6UL/apt_archive ./ InRelease Get:2 copy:/<>/resolver-fbJ6UL/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-fbJ6UL/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-fbJ6UL/apt_archive ./ Sources [552 B] Get:5 copy:/<>/resolver-fbJ6UL/apt_archive ./ Packages [623 B] Fetched 2138 B in 0s (67.5 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: g++-10 libstdc++-10-dev Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libgsl-dev libgsl25 libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu67 libio-pty-perl libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 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 libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 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 libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libgsl-dev libgsl25 libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu67 libio-pty-perl libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-bcftools-dummy tabix zlib1g-dev 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. Need to get 25.4 MB of archives. After this operation, 77.1 MB of additional disk space will be used. Get:1 copy:/<>/resolver-fbJ6UL/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [716 B] Get:2 http://ftpmaster.internal/ubuntu impish/main armhf bsdextrautils armhf 2.36.1-8ubuntu1 [80.7 kB] Get:3 http://ftpmaster.internal/ubuntu impish/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get:4 http://ftpmaster.internal/ubuntu impish/main armhf groff-base armhf 1.22.4-7 [870 kB] Get:5 http://ftpmaster.internal/ubuntu impish/main armhf libpipeline1 armhf 1.5.3-1 [23.3 kB] Get:6 http://ftpmaster.internal/ubuntu impish/main armhf man-db armhf 2.9.4-2 [1118 kB] Get:7 http://ftpmaster.internal/ubuntu impish/main armhf libelf1 armhf 0.185-1 [39.9 kB] Get:8 http://ftpmaster.internal/ubuntu impish/main armhf libicu67 armhf 67.1-7ubuntu1 [9788 kB] Get:9 http://ftpmaster.internal/ubuntu impish/main armhf libxml2 armhf 2.9.12+dfsg-4 [598 kB] Get:10 http://ftpmaster.internal/ubuntu impish/main armhf libmagic-mgc armhf 1:5.39-3 [228 kB] Get:11 http://ftpmaster.internal/ubuntu impish/main armhf libmagic1 armhf 1:5.39-3 [71.7 kB] Get:12 http://ftpmaster.internal/ubuntu impish/main armhf file armhf 1:5.39-3 [22.7 kB] Get:13 http://ftpmaster.internal/ubuntu impish/main armhf gettext-base armhf 0.21-4ubuntu3 [36.0 kB] Get:14 http://ftpmaster.internal/ubuntu impish/main armhf libpsl5 armhf 0.21.0-1.2 [52.3 kB] Get:15 http://ftpmaster.internal/ubuntu impish/main armhf libsigsegv2 armhf 2.13-1ubuntu1 [13.4 kB] Get:16 http://ftpmaster.internal/ubuntu impish/main armhf m4 armhf 1.4.18-5ubuntu1 [192 kB] Get:17 http://ftpmaster.internal/ubuntu impish/main armhf autoconf all 2.69-14 [293 kB] Get:18 http://ftpmaster.internal/ubuntu impish/main armhf autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:19 http://ftpmaster.internal/ubuntu impish/main armhf automake all 1:1.16.4-2 [557 kB] Get:20 http://ftpmaster.internal/ubuntu impish/main armhf autopoint all 0.21-4ubuntu3 [422 kB] Get:21 http://ftpmaster.internal/ubuntu impish/main armhf libdebhelper-perl all 13.3.4ubuntu2 [62.5 kB] Get:22 http://ftpmaster.internal/ubuntu impish/main armhf libtool all 2.4.6-15 [161 kB] Get:23 http://ftpmaster.internal/ubuntu impish/main armhf dh-autoreconf all 20 [16.1 kB] Get:24 http://ftpmaster.internal/ubuntu impish/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:25 http://ftpmaster.internal/ubuntu impish/main armhf libsub-override-perl all 0.09-2 [9532 B] Get:26 http://ftpmaster.internal/ubuntu impish/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [17.5 kB] Get:27 http://ftpmaster.internal/ubuntu impish/main armhf dh-strip-nondeterminism all 1.12.0-1 [5228 B] Get:28 http://ftpmaster.internal/ubuntu impish/main armhf libdw1 armhf 0.185-1 [198 kB] Get:29 http://ftpmaster.internal/ubuntu impish/main armhf debugedit armhf 1:5.0-0ubuntu2 [43.9 kB] Get:30 http://ftpmaster.internal/ubuntu impish/main armhf dwz armhf 0.14-1 [90.7 kB] Get:31 http://ftpmaster.internal/ubuntu impish/main armhf gettext armhf 0.21-4ubuntu3 [755 kB] Get:32 http://ftpmaster.internal/ubuntu impish/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu impish/main armhf po-debconf all 1.0.21+nmu1 [233 kB] Get:34 http://ftpmaster.internal/ubuntu impish/main armhf debhelper all 13.3.4ubuntu2 [921 kB] Get:35 http://ftpmaster.internal/ubuntu impish/main armhf libbrotli1 armhf 1.0.9-2build2 [259 kB] Get:36 http://ftpmaster.internal/ubuntu impish/main armhf libbz2-dev armhf 1.0.8-4ubuntu3 [27.8 kB] Get:37 http://ftpmaster.internal/ubuntu impish/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2.1build1 [13.2 kB] Get:38 http://ftpmaster.internal/ubuntu impish/main armhf libsasl2-2 armhf 2.1.27+dfsg-2.1build1 [42.4 kB] Get:39 http://ftpmaster.internal/ubuntu impish/main armhf libldap-2.5-0 armhf 2.5.6+dfsg-1~exp1ubuntu1 [162 kB] Get:40 http://ftpmaster.internal/ubuntu impish/main armhf libnghttp2-14 armhf 1.43.0-1 [61.2 kB] Get:41 http://ftpmaster.internal/ubuntu impish/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build2 [48.9 kB] Get:42 http://ftpmaster.internal/ubuntu impish/main armhf libssh-4 armhf 0.9.6-1 [163 kB] Get:43 http://ftpmaster.internal/ubuntu impish/main armhf libcurl3-gnutls armhf 7.74.0-1.3ubuntu2 [234 kB] Get:44 http://ftpmaster.internal/ubuntu impish/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3ubuntu2 [337 kB] Get:45 http://ftpmaster.internal/ubuntu impish/main armhf libdeflate0 armhf 1.7-2ubuntu2 [46.1 kB] Get:46 http://ftpmaster.internal/ubuntu impish/main armhf libdeflate-dev armhf 1.7-2ubuntu2 [40.4 kB] Get:47 http://ftpmaster.internal/ubuntu impish/universe armhf libgslcblas0 armhf 2.6+dfsg-2 [62.8 kB] Get:48 http://ftpmaster.internal/ubuntu impish/universe armhf libgsl25 armhf 2.6+dfsg-2 [743 kB] Get:49 http://ftpmaster.internal/ubuntu impish/universe armhf libgsl-dev armhf 2.6+dfsg-2 [964 kB] Get:50 http://ftpmaster.internal/ubuntu impish/universe armhf libhtscodecs2 armhf 1.1.1-2 [53.5 kB] Get:51 http://ftpmaster.internal/ubuntu impish/universe armhf libhts3 armhf 1.13+ds-2 [346 kB] Get:52 http://ftpmaster.internal/ubuntu impish/main armhf liblzma-dev armhf 5.2.5-2 [142 kB] Get:53 http://ftpmaster.internal/ubuntu impish/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2ubuntu7 [157 kB] Get:54 http://ftpmaster.internal/ubuntu impish/universe armhf libhts-dev armhf 1.13+ds-2 [4037 kB] Get:55 http://ftpmaster.internal/ubuntu impish/main armhf libio-pty-perl armhf 1:1.15-2 [31.9 kB] Get:56 http://ftpmaster.internal/ubuntu impish/universe armhf tabix armhf 1.13+ds-2 [320 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.4 MB in 1s (24.5 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 14697 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8ubuntu1_armhf.deb ... Unpacking bsdextrautils (2.36.1-8ubuntu1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-7_armhf.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../05-libelf1_0.185-1_armhf.deb ... Unpacking libelf1:armhf (0.185-1) ... 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Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_13.3.4ubuntu2_all.deb ... Unpacking debhelper (13.3.4ubuntu2) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../33-libbrotli1_1.0.9-2build2_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2build2) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../34-libbz2-dev_1.0.8-4ubuntu3_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.8-4ubuntu3) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../35-libsasl2-modules-db_2.1.27+dfsg-2.1build1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.27+dfsg-2.1build1) ... Selecting previously unselected package libsasl2-2:armhf. 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4ubuntu2) ... Setting up libbrotli1:armhf (1.0.9-2build2) ... Setting up libnghttp2-14:armhf (1.43.0-1) ... Setting up libmagic1:armhf (1:5.39-3) ... Setting up libdeflate0:armhf (1.7-2ubuntu2) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2.1build1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build2) ... Setting up libsigsegv2:armhf (2.13-1ubuntu1) ... Setting up autopoint (0.21-4ubuntu3) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2.1build1) ... Setting up libssh-4:armhf (0.9.6-1) ... Setting up liblzma-dev:armhf (5.2.5-2) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2ubuntu7) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdeflate-dev:armhf (1.7-2ubuntu2) ... Setting up tabix (1.13+ds-2) ... Setting up libelf1:armhf (0.185-1) ... Setting up libxml2:armhf (2.9.12+dfsg-4) ... Setting up libbz2-dev:armhf (1.0.8-4ubuntu3) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libdw1:armhf (0.185-1) ... Setting up gettext (0.21-4ubuntu3) ... Setting up libgsl-dev (2.6+dfsg-2) ... Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5ubuntu1) ... Setting up libldap-2.5-0:armhf (2.5.6+dfsg-1~exp1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-7) ... Setting up debugedit (1:5.0-0ubuntu2) ... Setting up automake (1:1.16.4-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:armhf (7.74.0-1.3ubuntu2) ... Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.3ubuntu2) ... Setting up man-db (2.9.4-2) ... 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 dh-autoreconf (20) ... Setting up libhts3:armhf (1.13+ds-2) ... Setting up libhts-dev:armhf (1.13+ds-2) ... Setting up debhelper (13.3.4ubuntu2) ... Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.34-0ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-159-generic arm64 (armv7l) Toolchain package versions: binutils_2.37-7ubuntu1 dpkg-dev_1.20.9ubuntu13 g++-10_10.3.0-11ubuntu1 g++-11_11.2.0-7ubuntu2 gcc-10_10.3.0-11ubuntu1 gcc-11_11.2.0-7ubuntu2 libc6-dev_2.34-0ubuntu2 libstdc++-10-dev_10.3.0-11ubuntu1 libstdc++-11-dev_11.2.0-7ubuntu2 libstdc++6_11.2.0-7ubuntu2 linux-libc-dev_5.13.0-16.16 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.9 autoconf_2.69-14 automake_1:1.16.4-2 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_11.1ubuntu3 base-passwd_3.5.51 bash_5.1-3ubuntu1 binutils_2.37-7ubuntu1 binutils-arm-linux-gnueabihf_2.37-7ubuntu1 binutils-common_2.37-7ubuntu1 bsdextrautils_2.36.1-8ubuntu1 bsdutils_1:2.36.1-8ubuntu1 build-essential_12.9ubuntu1 bzip2_1.0.8-4ubuntu3 ca-certificates_20210119ubuntu1 coreutils_8.32-4ubuntu2 cpp_4:11.2.0-1ubuntu1 cpp-10_10.3.0-11ubuntu1 cpp-11_11.2.0-7ubuntu2 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.3.4ubuntu2 debianutils_4.11.2 debugedit_1:5.0-0ubuntu2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.8-0ubuntu1 dpkg_1.20.9ubuntu13 dpkg-dev_1.20.9ubuntu13 dwz_0.14-1 e2fsprogs_1.46.3-1ubuntu3 fakeroot_1.25.3-1.1ubuntu2 file_1:5.39-3 findutils_4.8.0-1ubuntu2 g++_4:11.2.0-1ubuntu1 g++-10_10.3.0-11ubuntu1 g++-11_11.2.0-7ubuntu2 gcc_4:11.2.0-1ubuntu1 gcc-10_10.3.0-11ubuntu1 gcc-10-base_10.3.0-11ubuntu1 gcc-11_11.2.0-7ubuntu2 gcc-11-base_11.2.0-7ubuntu2 gettext_0.21-4ubuntu3 gettext-base_0.21-4ubuntu3 gpg_2.2.20-1ubuntu4 gpg-agent_2.2.20-1ubuntu4 gpgconf_2.2.20-1ubuntu4 gpgv_2.2.20-1ubuntu4 grep_3.7-0ubuntu1 groff-base_1.22.4-7 gzip_1.10-4ubuntu1 hostname_3.23 init_1.60 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10ubuntu1 libapparmor1_3.0.3-0ubuntu1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build21.04.0 libasan6_11.2.0-7ubuntu2 libassuan0_2.5.5-1 libatomic1_11.2.0-7ubuntu2 libattr1_1:2.4.48-6build1 libaudit-common_1:3.0-2ubuntu2 libaudit1_1:3.0-2ubuntu2 libbinutils_2.37-7ubuntu1 libblkid1_2.36.1-8ubuntu1 libbrotli1_1.0.9-2build2 libbz2-1.0_1.0.8-4ubuntu3 libbz2-dev_1.0.8-4ubuntu3 libc-bin_2.34-0ubuntu2 libc-dev-bin_2.34-0ubuntu2 libc6_2.34-0ubuntu2 libc6-dev_2.34-0ubuntu2 libcap-ng0_0.7.9-2.2build1 libcap2_1:2.44-1build1 libcc1-0_11.2.0-7ubuntu2 libcom-err2_1.46.3-1ubuntu3 libcrypt-dev_1:4.4.18-4ubuntu1 libcrypt1_1:4.4.18-4ubuntu1 libcryptsetup12_2:2.3.6-0ubuntu1 libctf-nobfd0_2.37-7ubuntu1 libctf0_2.37-7ubuntu1 libcurl3-gnutls_7.74.0-1.3ubuntu2 libcurl4-gnutls-dev_7.74.0-1.3ubuntu2 libdb5.3_5.3.28+dfsg1-0.8ubuntu1 libdebconfclient0_0.256ubuntu3 libdebhelper-perl_13.3.4ubuntu2 libdeflate-dev_1.7-2ubuntu2 libdeflate0_1.7-2ubuntu2 libdevmapper1.02.1_2:1.02.175-2.1ubuntu1 libdpkg-perl_1.20.9ubuntu13 libdw1_0.185-1 libelf1_0.185-1 libexpat1_2.4.1-2 libext2fs2_1.46.3-1ubuntu3 libfakeroot_1.25.3-1.1ubuntu2 libffi8_3.4.2-1ubuntu5 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-11ubuntu1 libgcc-11-dev_11.2.0-7ubuntu2 libgcc-s1_11.2.0-7ubuntu2 libgcrypt20_1.8.7-5ubuntu2 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgmp10_2:6.2.1+dfsg-1ubuntu2 libgnutls30_3.7.1-5ubuntu1 libgomp1_11.2.0-7ubuntu2 libgpg-error0_1.38-2build1 libgsl-dev_2.6+dfsg-2 libgsl25_2.6+dfsg-2 libgslcblas0_2.6+dfsg-2 libgssapi-krb5-2_1.18.3-6 libhogweed6_3.7.3-1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-2 libicu67_67.1-7ubuntu1 libidn2-0_2.3.1-1 libio-pty-perl_1:1.15-2 libip4tc2_1.8.7-1ubuntu2 libisl23_0.24-1 libjson-c5_0.15-2build2 libk5crypto3_1.18.3-6 libkeyutils1_1.6.1-2ubuntu1 libkmod2_28-1ubuntu4 libkrb5-3_1.18.3-6 libkrb5support0_1.18.3-6 libldap-2.5-0_2.5.6+dfsg-1~exp1ubuntu1 liblockfile-bin_1.17-1 liblockfile1_1.17-1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-8ubuntu1 libmpc3_1.2.0-1build1 libmpdec3_2.5.1-2 libmpfr6_4.1.0-3build1 libncurses6_6.2+20201114-2build1 libncursesw6_6.2+20201114-2build1 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.23.22-1build1 libpam-modules_1.3.1-5ubuntu11 libpam-modules-bin_1.3.1-5ubuntu11 libpam-runtime_1.3.1-5ubuntu11 libpam0g_1.3.1-5ubuntu11 libpcre2-8-0_10.37-0ubuntu2 libpcre3_2:8.39-13build3 libperl5.32_5.32.1-3ubuntu3 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3build3 libprocps8_2:3.3.17-5ubuntu3 libpsl5_0.21.0-1.2 libpython3-stdlib_3.9.4-1 libpython3.9-minimal_3.9.7-2build1 libpython3.9-stdlib_3.9.7-2build1 libreadline8_8.1-2 librtmp1_2.4+20151223.gitfa8646d.1-2build2 libsasl2-2_2.1.27+dfsg-2.1build1 libsasl2-modules-db_2.1.27+dfsg-2.1build1 libseccomp2_2.5.1-1ubuntu1 libselinux1_3.1-3build1 libsemanage-common_3.1-1ubuntu1 libsemanage1_3.1-1ubuntu1 libsepol1_3.1-1ubuntu1 libsigsegv2_2.13-1ubuntu1 libsmartcols1_2.36.1-8ubuntu1 libsqlite3-0_3.35.5-1 libss2_1.46.3-1ubuntu3 libssh-4_0.9.6-1 libssl1.1_1.1.1l-1ubuntu1 libstdc++-10-dev_10.3.0-11ubuntu1 libstdc++-11-dev_11.2.0-7ubuntu2 libstdc++6_11.2.0-7ubuntu2 libsub-override-perl_0.09-2 libsystemd0_248.3-1ubuntu7 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2build1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-7ubuntu2 libuchardet0_0.0.7-1 libudev1_248.3-1ubuntu7 libunistring2_0.9.10-6 libuuid1_2.36.1-8ubuntu1 libxml2_2.9.12+dfsg-4 libxxhash0_0.8.0-2 libzstd1_1.4.8+dfsg-2.1 linux-libc-dev_5.13.0-16.16 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu9 logsave_1.46.3-1ubuntu3 lsb-base_11.1.0ubuntu2 lto-disabled-list_16 m4_1.4.18-5ubuntu1 make_4.3-4ubuntu1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.36.1-8ubuntu1 ncurses-base_6.2+20201114-2build1 ncurses-bin_6.2+20201114-2build1 openssl_1.1.1l-1ubuntu1 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu9 patch_2.7.6-7 perl_5.32.1-3ubuntu3 perl-base_5.32.1-3ubuntu3 perl-modules-5.32_5.32.1-3ubuntu3 pinentry-curses_1.1.1-1 pkgbinarymangler_148 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-5ubuntu3 python3_3.9.4-1 python3-minimal_3.9.4-1 python3-psutil_5.8.0-1 python3.9_3.9.7-2build1 python3.9-minimal_3.9.7-2build1 readline-common_8.1-2 rpcsvc-proto_1.4.2-0ubuntu4 sbuild-build-depends-bcftools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.14 systemd_248.3-1ubuntu7 systemd-sysv_248.3-1ubuntu7 systemd-timesyncd_248.3-1ubuntu7 sysvinit-utils_2.96-7ubuntu1 tabix_1.13+ds-2 tar_1.34+dfsg-1build1 tzdata_2021a-2ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu1 util-linux_2.36.1-8ubuntu1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Oct 1 13:48:11 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_1.11-1.dsc dpkg-source: info: extracting bcftools in /<> dpkg-source: info: unpacking bcftools_1.11.orig.tar.gz dpkg-source: info: unpacking bcftools_1.11-1.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 disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym 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-22121190 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22121190 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22121190 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage.pl: info: source package bcftools dpkg-buildpackage.pl: info: source version 1.11-1 dpkg-buildpackage.pl: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage.pl: info: host architecture armhf 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/arm-linux-gnueabihf/bcftools ./configure --build=arm-linux-gnueabihf --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/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/arm-linux-gnueabihf/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... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for 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 "1.11"' > version.h gcc -Wall -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c bam2bcf_indel.c: In function ‘bcf_call_gap_prep’: bam2bcf_indel.c:338:37: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 338 | qq = (uint8_t*) calloc(qend - qbeg, 1); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:30, from /usr/include/htslib/hts.h:37, from bam2bcf_indel.c:29: /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ gcc -Wall -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/arm-linux-gnueabihf/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -ffile-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 -ffile-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 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -fPIC -shared -Wall -g -O2 -ffile-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 gcc -Wall -g -O2 -ffile-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 gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -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 extsort.o ccall.o em.o prob1.o kmin.o vcfplugin.o -lhts -lm -lz -lpthread 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/9wKauGSdk3/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/9wKauGSdk3/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/9wKauGSdk3/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/9wKauGSdk3/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/9wKauGSdk3/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/9wKauGSdk3/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/9wKauGSdk3/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/9wKauGSdk3/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/9wKauGSdk3/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/9wKauGSdk3/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/9wKauGSdk3/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/9wKauGSdk3/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/9wKauGSdk3/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/9wKauGSdk3/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/9wKauGSdk3/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/9wKauGSdk3/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/9wKauGSdk3/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/9wKauGSdk3/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/9wKauGSdk3/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/9wKauGSdk3/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/9wKauGSdk3/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/9wKauGSdk3/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/9wKauGSdk3/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/9wKauGSdk3/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/9wKauGSdk3/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/9wKauGSdk3/empty.bcf .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/9wKauGSdk3/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/check.1.chk /tmp/9wKauGSdk3/check.2.chk /tmp/9wKauGSdk3/check.3.chk /tmp/9wKauGSdk3/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/9wKauGSdk3/stats.a.vcf.gz /tmp/9wKauGSdk3/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/9wKauGSdk3/stats.a.vcf.gz /tmp/9wKauGSdk3/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/9wKauGSdk3/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/9wKauGSdk3/isec.a.vcf.gz /tmp/9wKauGSdk3/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/9wKauGSdk3/isec.a.vcf.gz /tmp/9wKauGSdk3/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/9wKauGSdk3/isec.a.vcf.gz /tmp/9wKauGSdk3/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/9wKauGSdk3/isec.a.vcf.gz /tmp/9wKauGSdk3/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/9wKauGSdk3/isec.a.vcf.gz /tmp/9wKauGSdk3/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/9wKauGSdk3/isec.a.vcf.gz /tmp/9wKauGSdk3/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/9wKauGSdk3/isec.a.vcf.gz /tmp/9wKauGSdk3/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/9wKauGSdk3/isec.a.vcf.gz /tmp/9wKauGSdk3/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/9wKauGSdk3/isec.a.vcf.gz /tmp/9wKauGSdk3/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/9wKauGSdk3/isec.a.vcf.gz /tmp/9wKauGSdk3/isec.b.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/9wKauGSdk3/isec.tab.gz /tmp/9wKauGSdk3/isec.a.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/9wKauGSdk3/isec.tab.gz /tmp/9wKauGSdk3/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/9wKauGSdk3/isec-miss.1.1.vcf.gz /tmp/9wKauGSdk3/isec-miss.1.2.vcf.gz /tmp/9wKauGSdk3/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/9wKauGSdk3/isec-miss.1.1.vcf.gz /tmp/9wKauGSdk3/isec-miss.1.2.vcf.gz /tmp/9wKauGSdk3/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/9wKauGSdk3/isec-miss.1.1.vcf.gz /tmp/9wKauGSdk3/isec-miss.1.2.vcf.gz /tmp/9wKauGSdk3/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/9wKauGSdk3/isec-miss.1.1.vcf.gz /tmp/9wKauGSdk3/isec-miss.1.2.vcf.gz /tmp/9wKauGSdk3/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/9wKauGSdk3/isec-miss.2.1.vcf.gz /tmp/9wKauGSdk3/isec-miss.2.2.vcf.gz /tmp/9wKauGSdk3/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/9wKauGSdk3/isec-miss.2.1.vcf.gz /tmp/9wKauGSdk3/isec-miss.2.2.vcf.gz /tmp/9wKauGSdk3/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/9wKauGSdk3/isec-miss.2.1.vcf.gz /tmp/9wKauGSdk3/isec-miss.2.2.vcf.gz /tmp/9wKauGSdk3/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/9wKauGSdk3/isec-miss.2.1.vcf.gz /tmp/9wKauGSdk3/isec-miss.2.2.vcf.gz /tmp/9wKauGSdk3/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AF:join /tmp/9wKauGSdk3/merge.join.a.vcf.gz /tmp/9wKauGSdk3/merge.join.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob -i AF:join /tmp/9wKauGSdk3/merge.join.a.vcf.gz /tmp/9wKauGSdk3/merge.join.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AF:join /tmp/9wKauGSdk3/merge.join.a.bcf /tmp/9wKauGSdk3/merge.join.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob -i AF:join /tmp/9wKauGSdk3/merge.join.a.bcf /tmp/9wKauGSdk3/merge.join.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/9wKauGSdk3/merge.LPL.a.vcf.gz /tmp/9wKauGSdk3/merge.LPL.b.vcf.gz /tmp/9wKauGSdk3/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/9wKauGSdk3/merge.LPL.a.vcf.gz /tmp/9wKauGSdk3/merge.LPL.b.vcf.gz /tmp/9wKauGSdk3/merge.LPL.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/9wKauGSdk3/merge.LPL.a.bcf /tmp/9wKauGSdk3/merge.LPL.b.bcf /tmp/9wKauGSdk3/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/9wKauGSdk3/merge.LPL.a.bcf /tmp/9wKauGSdk3/merge.LPL.b.bcf /tmp/9wKauGSdk3/merge.LPL.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 1 /tmp/9wKauGSdk3/merge.LPL.a.vcf.gz /tmp/9wKauGSdk3/merge.LPL.b.vcf.gz /tmp/9wKauGSdk3/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 1 /tmp/9wKauGSdk3/merge.LPL.a.vcf.gz /tmp/9wKauGSdk3/merge.LPL.b.vcf.gz /tmp/9wKauGSdk3/merge.LPL.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 1 /tmp/9wKauGSdk3/merge.LPL.a.bcf /tmp/9wKauGSdk3/merge.LPL.b.bcf /tmp/9wKauGSdk3/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 1 /tmp/9wKauGSdk3/merge.LPL.a.bcf /tmp/9wKauGSdk3/merge.LPL.b.bcf /tmp/9wKauGSdk3/merge.LPL.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 2 /tmp/9wKauGSdk3/merge.LPL.a.vcf.gz /tmp/9wKauGSdk3/merge.LPL.b.vcf.gz /tmp/9wKauGSdk3/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 2 /tmp/9wKauGSdk3/merge.LPL.a.vcf.gz /tmp/9wKauGSdk3/merge.LPL.b.vcf.gz /tmp/9wKauGSdk3/merge.LPL.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 2 /tmp/9wKauGSdk3/merge.LPL.a.bcf /tmp/9wKauGSdk3/merge.LPL.b.bcf /tmp/9wKauGSdk3/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 2 /tmp/9wKauGSdk3/merge.LPL.a.bcf /tmp/9wKauGSdk3/merge.LPL.b.bcf /tmp/9wKauGSdk3/merge.LPL.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 3 /tmp/9wKauGSdk3/merge.LPL.a.vcf.gz /tmp/9wKauGSdk3/merge.LPL.b.vcf.gz /tmp/9wKauGSdk3/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 3 /tmp/9wKauGSdk3/merge.LPL.a.vcf.gz /tmp/9wKauGSdk3/merge.LPL.b.vcf.gz /tmp/9wKauGSdk3/merge.LPL.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 3 /tmp/9wKauGSdk3/merge.LPL.a.bcf /tmp/9wKauGSdk3/merge.LPL.b.bcf /tmp/9wKauGSdk3/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 3 /tmp/9wKauGSdk3/merge.LPL.a.bcf /tmp/9wKauGSdk3/merge.LPL.b.bcf /tmp/9wKauGSdk3/merge.LPL.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 4 /tmp/9wKauGSdk3/merge.LPL.a.vcf.gz /tmp/9wKauGSdk3/merge.LPL.b.vcf.gz /tmp/9wKauGSdk3/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 4 /tmp/9wKauGSdk3/merge.LPL.a.vcf.gz /tmp/9wKauGSdk3/merge.LPL.b.vcf.gz /tmp/9wKauGSdk3/merge.LPL.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 4 /tmp/9wKauGSdk3/merge.LPL.a.bcf /tmp/9wKauGSdk3/merge.LPL.b.bcf /tmp/9wKauGSdk3/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 4 /tmp/9wKauGSdk3/merge.LPL.a.bcf /tmp/9wKauGSdk3/merge.LPL.b.bcf /tmp/9wKauGSdk3/merge.LPL.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 5 /tmp/9wKauGSdk3/merge.LPL.a.vcf.gz /tmp/9wKauGSdk3/merge.LPL.b.vcf.gz /tmp/9wKauGSdk3/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 5 /tmp/9wKauGSdk3/merge.LPL.a.vcf.gz /tmp/9wKauGSdk3/merge.LPL.b.vcf.gz /tmp/9wKauGSdk3/merge.LPL.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 5 /tmp/9wKauGSdk3/merge.LPL.a.bcf /tmp/9wKauGSdk3/merge.LPL.b.bcf /tmp/9wKauGSdk3/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 5 /tmp/9wKauGSdk3/merge.LPL.a.bcf /tmp/9wKauGSdk3/merge.LPL.b.bcf /tmp/9wKauGSdk3/merge.LPL.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/9wKauGSdk3/merge.a.vcf.gz /tmp/9wKauGSdk3/merge.b.vcf.gz /tmp/9wKauGSdk3/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/9wKauGSdk3/merge.a.vcf.gz /tmp/9wKauGSdk3/merge.b.vcf.gz /tmp/9wKauGSdk3/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/9wKauGSdk3/merge.a.bcf /tmp/9wKauGSdk3/merge.b.bcf /tmp/9wKauGSdk3/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/9wKauGSdk3/merge.a.bcf /tmp/9wKauGSdk3/merge.b.bcf /tmp/9wKauGSdk3/merge.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/9wKauGSdk3/merge.a.vcf.gz /tmp/9wKauGSdk3/merge.b.vcf.gz /tmp/9wKauGSdk3/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -Fx /tmp/9wKauGSdk3/merge.a.vcf.gz /tmp/9wKauGSdk3/merge.b.vcf.gz /tmp/9wKauGSdk3/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/9wKauGSdk3/merge.a.bcf /tmp/9wKauGSdk3/merge.b.bcf /tmp/9wKauGSdk3/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -Fx /tmp/9wKauGSdk3/merge.a.bcf /tmp/9wKauGSdk3/merge.b.bcf /tmp/9wKauGSdk3/merge.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/9wKauGSdk3/merge.a.vcf.gz /tmp/9wKauGSdk3/merge.b.vcf.gz /tmp/9wKauGSdk3/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -0 /tmp/9wKauGSdk3/merge.a.vcf.gz /tmp/9wKauGSdk3/merge.b.vcf.gz /tmp/9wKauGSdk3/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/9wKauGSdk3/merge.a.bcf /tmp/9wKauGSdk3/merge.b.bcf /tmp/9wKauGSdk3/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -0 /tmp/9wKauGSdk3/merge.a.bcf /tmp/9wKauGSdk3/merge.b.bcf /tmp/9wKauGSdk3/merge.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/9wKauGSdk3/merge.2.a.vcf.gz /tmp/9wKauGSdk3/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m none /tmp/9wKauGSdk3/merge.2.a.vcf.gz /tmp/9wKauGSdk3/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/9wKauGSdk3/merge.2.a.bcf /tmp/9wKauGSdk3/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m none /tmp/9wKauGSdk3/merge.2.a.bcf /tmp/9wKauGSdk3/merge.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/9wKauGSdk3/merge.2.a.vcf.gz /tmp/9wKauGSdk3/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m both /tmp/9wKauGSdk3/merge.2.a.vcf.gz /tmp/9wKauGSdk3/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/9wKauGSdk3/merge.2.a.bcf /tmp/9wKauGSdk3/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m both /tmp/9wKauGSdk3/merge.2.a.bcf /tmp/9wKauGSdk3/merge.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/9wKauGSdk3/merge.2.a.vcf.gz /tmp/9wKauGSdk3/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m all /tmp/9wKauGSdk3/merge.2.a.vcf.gz /tmp/9wKauGSdk3/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/9wKauGSdk3/merge.2.a.bcf /tmp/9wKauGSdk3/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m all /tmp/9wKauGSdk3/merge.2.a.bcf /tmp/9wKauGSdk3/merge.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/9wKauGSdk3/merge.3.a.vcf.gz /tmp/9wKauGSdk3/merge.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/9wKauGSdk3/merge.3.a.vcf.gz /tmp/9wKauGSdk3/merge.3.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/9wKauGSdk3/merge.3.a.bcf /tmp/9wKauGSdk3/merge.3.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/9wKauGSdk3/merge.3.a.bcf /tmp/9wKauGSdk3/merge.3.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/9wKauGSdk3/merge.4.a.vcf.gz /tmp/9wKauGSdk3/merge.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m id /tmp/9wKauGSdk3/merge.4.a.vcf.gz /tmp/9wKauGSdk3/merge.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/9wKauGSdk3/merge.4.a.bcf /tmp/9wKauGSdk3/merge.4.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m id /tmp/9wKauGSdk3/merge.4.a.bcf /tmp/9wKauGSdk3/merge.4.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/9wKauGSdk3/gvcf.merge.1.vcf.gz /tmp/9wKauGSdk3/gvcf.merge.2.vcf.gz /tmp/9wKauGSdk3/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/9wKauGSdk3/gvcf.merge.1.vcf.gz /tmp/9wKauGSdk3/gvcf.merge.2.vcf.gz /tmp/9wKauGSdk3/gvcf.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/9wKauGSdk3/gvcf.merge.1.bcf /tmp/9wKauGSdk3/gvcf.merge.2.bcf /tmp/9wKauGSdk3/gvcf.merge.3.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/9wKauGSdk3/gvcf.merge.1.bcf /tmp/9wKauGSdk3/gvcf.merge.2.bcf /tmp/9wKauGSdk3/gvcf.merge.3.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/9wKauGSdk3/merge.gvcf.2.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.2.b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/9wKauGSdk3/merge.gvcf.2.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.2.b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.2.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - -i SRC:join /tmp/9wKauGSdk3/merge.gvcf.3.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/9wKauGSdk3/merge.gvcf.3.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/9wKauGSdk3/merge.gvcf.4.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/9wKauGSdk3/merge.gvcf.4.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/9wKauGSdk3/merge.gvcf.4.a.bcf /tmp/9wKauGSdk3/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/9wKauGSdk3/merge.gvcf.4.a.bcf /tmp/9wKauGSdk3/merge.gvcf.4.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/9wKauGSdk3/merge.5.a.vcf.gz /tmp/9wKauGSdk3/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/9wKauGSdk3/merge.5.a.vcf.gz /tmp/9wKauGSdk3/merge.5.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/9wKauGSdk3/merge.5.a.bcf /tmp/9wKauGSdk3/merge.5.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/9wKauGSdk3/merge.5.a.bcf /tmp/9wKauGSdk3/merge.5.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/9wKauGSdk3/merge.6.a.vcf.gz /tmp/9wKauGSdk3/merge.6.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/9wKauGSdk3/merge.6.a.vcf.gz /tmp/9wKauGSdk3/merge.6.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/9wKauGSdk3/merge.6.a.bcf /tmp/9wKauGSdk3/merge.6.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/9wKauGSdk3/merge.6.a.bcf /tmp/9wKauGSdk3/merge.6.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/9wKauGSdk3/merge.gvcf.7.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/9wKauGSdk3/merge.gvcf.7.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.7.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/9wKauGSdk3/merge.gvcf.7.a.bcf /tmp/9wKauGSdk3/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/9wKauGSdk3/merge.gvcf.7.a.bcf /tmp/9wKauGSdk3/merge.gvcf.7.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/9wKauGSdk3/merge.gvcf.8.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/9wKauGSdk3/merge.gvcf.8.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.8.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/9wKauGSdk3/merge.gvcf.8.a.bcf /tmp/9wKauGSdk3/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/9wKauGSdk3/merge.gvcf.8.a.bcf /tmp/9wKauGSdk3/merge.gvcf.8.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/9wKauGSdk3/merge.7.a.vcf.gz /tmp/9wKauGSdk3/merge.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/9wKauGSdk3/merge.7.a.vcf.gz /tmp/9wKauGSdk3/merge.7.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/9wKauGSdk3/merge.7.a.bcf /tmp/9wKauGSdk3/merge.7.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/9wKauGSdk3/merge.7.a.bcf /tmp/9wKauGSdk3/merge.7.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/9wKauGSdk3/merge.gvcf.9a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9c.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa /tmp/9wKauGSdk3/merge.gvcf.9a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9c.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9d.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/9wKauGSdk3/merge.gvcf.9a.bcf /tmp/9wKauGSdk3/merge.gvcf.9b.bcf /tmp/9wKauGSdk3/merge.gvcf.9c.bcf /tmp/9wKauGSdk3/merge.gvcf.9d.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa /tmp/9wKauGSdk3/merge.gvcf.9a.bcf /tmp/9wKauGSdk3/merge.gvcf.9b.bcf /tmp/9wKauGSdk3/merge.gvcf.9c.bcf /tmp/9wKauGSdk3/merge.gvcf.9d.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/9wKauGSdk3/merge.gvcf.9a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9c.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/9wKauGSdk3/merge.gvcf.9a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9c.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9d.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/9wKauGSdk3/merge.gvcf.9a.bcf /tmp/9wKauGSdk3/merge.gvcf.9b.bcf /tmp/9wKauGSdk3/merge.gvcf.9c.bcf /tmp/9wKauGSdk3/merge.gvcf.9d.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/9wKauGSdk3/merge.gvcf.9a.bcf /tmp/9wKauGSdk3/merge.gvcf.9b.bcf /tmp/9wKauGSdk3/merge.gvcf.9c.bcf /tmp/9wKauGSdk3/merge.gvcf.9d.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/9wKauGSdk3/merge.gvcf.9a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9c.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9d.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa /tmp/9wKauGSdk3/merge.gvcf.9a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9c.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9d.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9e.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/9wKauGSdk3/merge.gvcf.9a.bcf /tmp/9wKauGSdk3/merge.gvcf.9b.bcf /tmp/9wKauGSdk3/merge.gvcf.9c.bcf /tmp/9wKauGSdk3/merge.gvcf.9d.bcf /tmp/9wKauGSdk3/merge.gvcf.9e.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa /tmp/9wKauGSdk3/merge.gvcf.9a.bcf /tmp/9wKauGSdk3/merge.gvcf.9b.bcf /tmp/9wKauGSdk3/merge.gvcf.9c.bcf /tmp/9wKauGSdk3/merge.gvcf.9d.bcf /tmp/9wKauGSdk3/merge.gvcf.9e.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/9wKauGSdk3/merge.gvcf.9a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9c.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9d.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/9wKauGSdk3/merge.gvcf.9a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9c.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9d.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.9e.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/9wKauGSdk3/merge.gvcf.9a.bcf /tmp/9wKauGSdk3/merge.gvcf.9b.bcf /tmp/9wKauGSdk3/merge.gvcf.9c.bcf /tmp/9wKauGSdk3/merge.gvcf.9d.bcf /tmp/9wKauGSdk3/merge.gvcf.9e.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/9wKauGSdk3/merge.gvcf.9a.bcf /tmp/9wKauGSdk3/merge.gvcf.9b.bcf /tmp/9wKauGSdk3/merge.gvcf.9c.bcf /tmp/9wKauGSdk3/merge.gvcf.9d.bcf /tmp/9wKauGSdk3/merge.gvcf.9e.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/9wKauGSdk3/merge.gvcf.10.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/9wKauGSdk3/merge.gvcf.10.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.10.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/9wKauGSdk3/merge.gvcf.10.a.bcf /tmp/9wKauGSdk3/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/9wKauGSdk3/merge.gvcf.10.a.bcf /tmp/9wKauGSdk3/merge.gvcf.10.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/9wKauGSdk3/merge.gvcf.10.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob -m none /tmp/9wKauGSdk3/merge.gvcf.10.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.10.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/9wKauGSdk3/merge.gvcf.10.a.bcf /tmp/9wKauGSdk3/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob -m none /tmp/9wKauGSdk3/merge.gvcf.10.a.bcf /tmp/9wKauGSdk3/merge.gvcf.10.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa /tmp/9wKauGSdk3/merge.gvcf.10.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa /tmp/9wKauGSdk3/merge.gvcf.10.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.10.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa /tmp/9wKauGSdk3/merge.gvcf.10.a.bcf /tmp/9wKauGSdk3/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa /tmp/9wKauGSdk3/merge.gvcf.10.a.bcf /tmp/9wKauGSdk3/merge.gvcf.10.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa -m none /tmp/9wKauGSdk3/merge.gvcf.10.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/9wKauGSdk3/merge.gvcf.10.a.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.10.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa -m none /tmp/9wKauGSdk3/merge.gvcf.10.a.bcf /tmp/9wKauGSdk3/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/9wKauGSdk3/merge.gvcf.10.a.bcf /tmp/9wKauGSdk3/merge.gvcf.10.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa /tmp/9wKauGSdk3/merge.gvcf.10.b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa /tmp/9wKauGSdk3/merge.gvcf.10.b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.10.a.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa /tmp/9wKauGSdk3/merge.gvcf.10.b.bcf /tmp/9wKauGSdk3/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa /tmp/9wKauGSdk3/merge.gvcf.10.b.bcf /tmp/9wKauGSdk3/merge.gvcf.10.a.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa -m none /tmp/9wKauGSdk3/merge.gvcf.10.b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/9wKauGSdk3/merge.gvcf.10.b.vcf.gz /tmp/9wKauGSdk3/merge.gvcf.10.a.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa -m none /tmp/9wKauGSdk3/merge.gvcf.10.b.bcf /tmp/9wKauGSdk3/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/9wKauGSdk3/merge.gvcf.10.b.bcf /tmp/9wKauGSdk3/merge.gvcf.10.a.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/9wKauGSdk3/merge.noidx.a.vcf.gz /tmp/9wKauGSdk3/merge.noidx.b.vcf.gz /tmp/9wKauGSdk3/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/9wKauGSdk3/merge.noidx.a.vcf.gz /tmp/9wKauGSdk3/merge.noidx.b.vcf.gz /tmp/9wKauGSdk3/merge.noidx.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/9wKauGSdk3/merge.noidx.a.bcf /tmp/9wKauGSdk3/merge.noidx.b.bcf /tmp/9wKauGSdk3/merge.noidx.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/9wKauGSdk3/merge.noidx.a.bcf /tmp/9wKauGSdk3/merge.noidx.b.bcf /tmp/9wKauGSdk3/merge.noidx.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --no-index /<>/test/merge.noidx.a.vcf /<>/test/merge.noidx.b.vcf /<>/test/merge.noidx.c.vcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --no-index /<>/test/merge.noidx.a.vcf /<>/test/merge.noidx.b.vcf /<>/test/merge.noidx.c.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --no-index /tmp/9wKauGSdk3/merge.noidx.a.bcf /tmp/9wKauGSdk3/merge.noidx.b.bcf /tmp/9wKauGSdk3/merge.noidx.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --no-index /tmp/9wKauGSdk3/merge.noidx.a.bcf /tmp/9wKauGSdk3/merge.noidx.b.bcf /tmp/9wKauGSdk3/merge.noidx.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/9wKauGSdk3/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/query.string.vcf.gz | /<>/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/9wKauGSdk3/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/query.string.vcf.gz | /<>/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/9wKauGSdk3/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/query.string.vcf.gz | /<>/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.variantkey.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/query.variantkey.vcf.gz | /<>/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/missing.vcf.gz | /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/9wKauGSdk3/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/filter.11.vcf.gz | /<>/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/9wKauGSdk3/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/filter.11.vcf.gz | /<>/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/9wKauGSdk3/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/filter.11.vcf.gz | /<>/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/9wKauGSdk3/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/filter.11.vcf.gz | /<>/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/9wKauGSdk3/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.4.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/view.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.6.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/query.filter.10.vcf.gz | /<>/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /<>/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/9wKauGSdk3/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/9wKauGSdk3/query.vcf.gz | /<>/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_norm: /<>/bcftools norm --no-version -cx -f /<>/test/norm.fa /tmp/9wKauGSdk3/norm.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -cx -f /<>/test/norm.fa /tmp/9wKauGSdk3/norm.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/9wKauGSdk3/norm.split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/9wKauGSdk3/norm.split.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/9wKauGSdk3/norm.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/9wKauGSdk3/norm.split.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --force /tmp/9wKauGSdk3/norm.split.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- --force /tmp/9wKauGSdk3/norm.split.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/9wKauGSdk3/norm.split.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/9wKauGSdk3/norm.split.4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --keep-sum AD /tmp/9wKauGSdk3/norm.split.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- --keep-sum AD /tmp/9wKauGSdk3/norm.split.4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- -f /<>/test/norm.fa /tmp/9wKauGSdk3/norm.split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- -f /<>/test/norm.fa /tmp/9wKauGSdk3/norm.split.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/9wKauGSdk3/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/9wKauGSdk3/norm.merge.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/9wKauGSdk3/norm.merge.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/9wKauGSdk3/norm.merge.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/9wKauGSdk3/norm.merge.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/9wKauGSdk3/norm.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/9wKauGSdk3/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ -s /tmp/9wKauGSdk3/norm.merge.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -Nc s -f /<>/test/norm.fa /tmp/9wKauGSdk3/norm.setref.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -Nc s -f /<>/test/norm.fa /tmp/9wKauGSdk3/norm.setref.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.fa /tmp/9wKauGSdk3/norm.telomere.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/9wKauGSdk3/norm.telomere.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/9wKauGSdk3/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d snps /tmp/9wKauGSdk3/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/9wKauGSdk3/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d indels /tmp/9wKauGSdk3/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/9wKauGSdk3/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d both /tmp/9wKauGSdk3/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/9wKauGSdk3/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d all /tmp/9wKauGSdk3/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/9wKauGSdk3/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d none /tmp/9wKauGSdk3/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/9wKauGSdk3/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d exact /tmp/9wKauGSdk3/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/9wKauGSdk3/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d none /tmp/9wKauGSdk3/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/9wKauGSdk3/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d exact /tmp/9wKauGSdk3/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/9wKauGSdk3/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d indels /tmp/9wKauGSdk3/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d any /tmp/9wKauGSdk3/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d any /tmp/9wKauGSdk3/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/9wKauGSdk3/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d both /tmp/9wKauGSdk3/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/9wKauGSdk3/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d snps /tmp/9wKauGSdk3/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.2.fa /tmp/9wKauGSdk3/norm.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.2.fa /tmp/9wKauGSdk3/norm.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s -f /<>/test/norm.iupac.fa /tmp/9wKauGSdk3/norm.iupac.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -c s -f /<>/test/norm.iupac.fa /tmp/9wKauGSdk3/norm.iupac.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s -f /<>/test/norm.3.fa /tmp/9wKauGSdk3/norm.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -c s -f /<>/test/norm.3.fa /tmp/9wKauGSdk3/norm.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/9wKauGSdk3/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/9wKauGSdk3/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/9wKauGSdk3/view.vcf.gz -r20,Y .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/9wKauGSdk3/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/9wKauGSdk3/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -p /tmp/9wKauGSdk3/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/9wKauGSdk3/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -P /tmp/9wKauGSdk3/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/9wKauGSdk3/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/9wKauGSdk3/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/9wKauGSdk3/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/9wKauGSdk3/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/9wKauGSdk3/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/9wKauGSdk3/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/9wKauGSdk3/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/9wKauGSdk3/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/9wKauGSdk3/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/9wKauGSdk3/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/9wKauGSdk3/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/9wKauGSdk3/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/9wKauGSdk3/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/9wKauGSdk3/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/9wKauGSdk3/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/9wKauGSdk3/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/9wKauGSdk3/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/9wKauGSdk3/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/9wKauGSdk3/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asB /tmp/9wKauGSdk3/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/9wKauGSdk3/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/9wKauGSdk3/view.vectors.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/9wKauGSdk3/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/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/9wKauGSdk3/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/9wKauGSdk3/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/9wKauGSdk3/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/9wKauGSdk3/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/9wKauGSdk3/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/9wKauGSdk3/idx.1.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/9wKauGSdk3/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.2.bed /tmp/9wKauGSdk3/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.3.bed /tmp/9wKauGSdk3/idx.3.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.4.bed /tmp/9wKauGSdk3/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_view: /<>/bcftools view --no-version -H -C5:nonmajor /tmp/9wKauGSdk3/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/9wKauGSdk3/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/9wKauGSdk3/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/9wKauGSdk3/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/9wKauGSdk3/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/9wKauGSdk3/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/9wKauGSdk3/mpileup.tab.gz /<>/test/mpileup.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/9wKauGSdk3/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/9wKauGSdk3/mpileup.2.tab.gz /<>/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/9wKauGSdk3/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/9wKauGSdk3/mpileup.3.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/9wKauGSdk3/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/9wKauGSdk3/mpileup.4.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/9wKauGSdk3/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/9wKauGSdk3/mpileup.5.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/9wKauGSdk3/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/9wKauGSdk3/mpileup.6.tab.gz -i /<>/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/9wKauGSdk3/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/9wKauGSdk3/mpileup.7.tab.gz -i /<>/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/9wKauGSdk3/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/9wKauGSdk3/mpileup.cals.1.tab.gz /<>/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/9wKauGSdk3/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/9wKauGSdk3/mpileup.cals.2.tab.gz /<>/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/9wKauGSdk3/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 -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_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_filter: /<>/bcftools filter -mx -s + -g2:mnp,indel,other /<>/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /<>/test/filter.7.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'FORMAT/AO==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i 'QUAL/FMT/AD==55' /<>/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /<>/test/filter.9.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i 'QUAL/INFO/AD==10' /<>/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /<>/test/filter.9.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'ABS(AO[1:])==2' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /<>/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /<>/test/filter.10.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /<>/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /<>/test/filter.10.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /<>/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /<>/test/filter.10.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /<>/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /<>/test/filter.10.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. 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/9wKauGSdk3/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/9wKauGSdk3/regions.tab.gz /tmp/9wKauGSdk3/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/9wKauGSdk3/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/9wKauGSdk3/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/9wKauGSdk3/regions.tab.gz /tmp/9wKauGSdk3/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/9wKauGSdk3/regions.bed /tmp/9wKauGSdk3/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/9wKauGSdk3/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/9wKauGSdk3/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/9wKauGSdk3/regions.bed /tmp/9wKauGSdk3/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/9wKauGSdk3/regions.bed.gz /tmp/9wKauGSdk3/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/9wKauGSdk3/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/9wKauGSdk3/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/9wKauGSdk3/regions.bed.gz /tmp/9wKauGSdk3/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/9wKauGSdk3/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/9wKauGSdk3/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/9wKauGSdk3/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/9wKauGSdk3/annots4.vcf.gz -c +INFO /tmp/9wKauGSdk3/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots4.vcf.gz -c +INFO /tmp/9wKauGSdk3/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annots11.vcf.gz -c FMT /tmp/9wKauGSdk3/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots11.vcf.gz -c FMT /tmp/9wKauGSdk3/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annots2.vcf.gz -c FMT/newGT:=GT /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots2.vcf.gz -c FMT/newGT:=GT /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annots12.vcf.gz -c FMT/GT:=newGT /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annots12.vcf.gz -c FMT/GT:=newGT /tmp/9wKauGSdk3/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/9wKauGSdk3/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/9wKauGSdk3/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/9wKauGSdk3/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/9wKauGSdk3/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annotate20.src.vcf.gz -c FMT/GT /tmp/9wKauGSdk3/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annotate20.src.vcf.gz -c FMT/GT /tmp/9wKauGSdk3/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annotate20.src.vcf.gz -c +FMT/GT /tmp/9wKauGSdk3/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annotate20.src.vcf.gz -c +FMT/GT /tmp/9wKauGSdk3/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annotate20.src.vcf.gz -c -FMT/GT /tmp/9wKauGSdk3/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annotate20.src.vcf.gz -c -FMT/GT /tmp/9wKauGSdk3/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /<>/test/annotate.multi.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/9wKauGSdk3/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /<>/test/annotate.multi.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/9wKauGSdk3/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/9wKauGSdk3/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/9wKauGSdk3/concat.1.a.vcf.gz /tmp/9wKauGSdk3/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/9wKauGSdk3/concat.1.a.vcf.gz /tmp/9wKauGSdk3/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/9wKauGSdk3/concat.1.a.bcf /tmp/9wKauGSdk3/concat.1.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/9wKauGSdk3/concat.1.a.bcf /tmp/9wKauGSdk3/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/9wKauGSdk3/concat.2.a.vcf.gz /tmp/9wKauGSdk3/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/9wKauGSdk3/concat.2.a.vcf.gz /tmp/9wKauGSdk3/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/9wKauGSdk3/concat.2.a.bcf /tmp/9wKauGSdk3/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/9wKauGSdk3/concat.2.a.bcf /tmp/9wKauGSdk3/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/9wKauGSdk3/concat.2.a.vcf.gz /tmp/9wKauGSdk3/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/9wKauGSdk3/concat.2.a.vcf.gz /tmp/9wKauGSdk3/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/9wKauGSdk3/concat.2.a.bcf /tmp/9wKauGSdk3/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/9wKauGSdk3/concat.2.a.bcf /tmp/9wKauGSdk3/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/9wKauGSdk3/concat.3.a.vcf.gz /tmp/9wKauGSdk3/concat.3.b.vcf.gz /tmp/9wKauGSdk3/concat.3.0.vcf.gz /tmp/9wKauGSdk3/concat.3.c.vcf.gz /tmp/9wKauGSdk3/concat.3.d.vcf.gz /tmp/9wKauGSdk3/concat.3.e.vcf.gz /tmp/9wKauGSdk3/concat.3.f.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/9wKauGSdk3/concat.3.a.vcf.gz /tmp/9wKauGSdk3/concat.3.b.vcf.gz /tmp/9wKauGSdk3/concat.3.0.vcf.gz /tmp/9wKauGSdk3/concat.3.c.vcf.gz /tmp/9wKauGSdk3/concat.3.d.vcf.gz /tmp/9wKauGSdk3/concat.3.e.vcf.gz /tmp/9wKauGSdk3/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/9wKauGSdk3/concat.3.a.bcf /tmp/9wKauGSdk3/concat.3.b.bcf /tmp/9wKauGSdk3/concat.3.0.bcf /tmp/9wKauGSdk3/concat.3.c.bcf /tmp/9wKauGSdk3/concat.3.d.bcf /tmp/9wKauGSdk3/concat.3.e.bcf /tmp/9wKauGSdk3/concat.3.f.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/9wKauGSdk3/concat.3.a.bcf /tmp/9wKauGSdk3/concat.3.b.bcf /tmp/9wKauGSdk3/concat.3.0.bcf /tmp/9wKauGSdk3/concat.3.c.bcf /tmp/9wKauGSdk3/concat.3.d.bcf /tmp/9wKauGSdk3/concat.3.e.bcf /tmp/9wKauGSdk3/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1649403068 .. ok test_naive_concat: /<>/bcftools concat --naive-force /tmp/9wKauGSdk3/naive_concat.0.bcf /tmp/9wKauGSdk3/naive_concat.1.bcf /tmp/9wKauGSdk3/naive_concat.2.bcf /tmp/9wKauGSdk3/naive_concat.3.bcf /tmp/9wKauGSdk3/naive_concat.4.bcf /tmp/9wKauGSdk3/naive_concat.5.bcf /tmp/9wKauGSdk3/naive_concat.6.bcf /tmp/9wKauGSdk3/naive_concat.7.bcf /tmp/9wKauGSdk3/naive_concat.8.bcf /tmp/9wKauGSdk3/naive_concat.9.bcf | /<>/bcftools view -H .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/9wKauGSdk3/naive_concat.0.vcf.gz /tmp/9wKauGSdk3/naive_concat.1.vcf.gz /tmp/9wKauGSdk3/naive_concat.2.vcf.gz /tmp/9wKauGSdk3/naive_concat.3.vcf.gz /tmp/9wKauGSdk3/naive_concat.4.vcf.gz /tmp/9wKauGSdk3/naive_concat.5.vcf.gz /tmp/9wKauGSdk3/naive_concat.6.vcf.gz /tmp/9wKauGSdk3/naive_concat.7.vcf.gz /tmp/9wKauGSdk3/naive_concat.8.vcf.gz /tmp/9wKauGSdk3/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/9wKauGSdk3/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/9wKauGSdk3/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/9wKauGSdk3/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/9wKauGSdk3/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/9wKauGSdk3/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/9wKauGSdk3/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/9wKauGSdk3/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/9wKauGSdk3/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/9wKauGSdk3/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/9wKauGSdk3/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/9wKauGSdk3/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/9wKauGSdk3/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/9wKauGSdk3/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/9wKauGSdk3/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/9wKauGSdk3/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/9wKauGSdk3/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/9wKauGSdk3/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/9wKauGSdk3/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/9wKauGSdk3/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/9wKauGSdk3/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/9wKauGSdk3/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/9wKauGSdk3/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/9wKauGSdk3/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/9wKauGSdk3/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/9wKauGSdk3/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.fai /tmp/9wKauGSdk3/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/9wKauGSdk3/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.2.hdr -f /<>/test/reheader.fai /tmp/9wKauGSdk3/reheader.2.vcf.gz | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/9wKauGSdk3/rename.map -Ov /tmp/9wKauGSdk3/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/9wKauGSdk3/rename.map -Ob /tmp/9wKauGSdk3/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/9wKauGSdk3/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/9wKauGSdk3/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/9wKauGSdk3/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/convert.vcf.gz | /<>/bcftools convert -g -,. .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/9wKauGSdk3/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/convert.vcf.gz | /<>/bcftools convert -g .,- .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/9wKauGSdk3/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/9wKauGSdk3/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/9wKauGSdk3/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/9wKauGSdk3/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/9wKauGSdk3/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/check.vcf.gz | /<>/bcftools convert -g -,. --chrom .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom /tmp/9wKauGSdk3/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/check.vcf.gz | /<>/bcftools convert -g .,- --chrom .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/9wKauGSdk3/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/check.vcf.gz | /<>/bcftools convert -g -,. --chrom --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/9wKauGSdk3/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/9wKauGSdk3/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/convert.vcf.gz | /<>/bcftools convert -h -,.,. .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/9wKauGSdk3/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/convert.vcf.gz | /<>/bcftools convert -h .,-,. .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/9wKauGSdk3/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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_hls2vcf: /<>/bcftools convert --vcf-ids -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 --vcf-ids -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_hs2vcf: /<>/bcftools convert --vcf-ids --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --vcf-ids --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples -Ou | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/9wKauGSdk3/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/convert.vcf.gz | /<>/bcftools convert --hapsample -,. .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/9wKauGSdk3/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/convert.vcf.gz | /<>/bcftools convert --hapsample .,- .. ok test_vcf_convert: /<>/bcftools convert --haplegendsample -,.,. /tmp/9wKauGSdk3/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/9wKauGSdk3/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/9wKauGSdk3/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/9wKauGSdk3/consensus.1.chain.new >/dev/null; cat /tmp/9wKauGSdk3/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/9wKauGSdk3/consensus.2.chain.new >/dev/null; cat /tmp/9wKauGSdk3/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab -c /tmp/9wKauGSdk3/consensus.3.chain.new >/dev/null; cat /tmp/9wKauGSdk3/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/9wKauGSdk3/consensus.4.chain.new >/dev/null; cat /tmp/9wKauGSdk3/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/empty.vcf.gz -f /<>/test/consensus.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus4.vcf.gz -f /<>/test/consensus2.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus5.vcf.gz -f /<>/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus6.vcf.gz -f /<>/test/consensus6.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus8.vcf.gz -f /<>/test/consensus.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus8.vcf.gz -f /<>/test/consensus.fa -a . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus8.vcf.gz -f /<>/test/consensus.fa -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus8.vcf.gz -f /<>/test/consensus.fa -a . -i 'ALT!=""' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus8.vcf.gz -f /<>/test/consensus.fa -a . -e 'MinDP>15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus8.vcf.gz -f /<>/test/consensus.fa -a . -e 'MinDP<15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.9.vcf.gz -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.9.vcf.gz -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.10.vcf.gz -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.10.vcf.gz -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.11.vcf.gz -f /<>/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.11.vcf.gz -f /<>/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.12.vcf.gz -f /<>/test/consensus.12.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/9wKauGSdk3/consensus.13.vcf.gz -f /<>/test/consensus.13.fa .. 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 The outputs differ: /<>/test/mpileup/mpileup.1.out /<>/test/mpileup/mpileup.1.out.new [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL 0,27,189 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL 0,27,188 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL 0,24,189 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL 0,24,178 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL 0,27,170 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL 0,30,190 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL 0,27,192 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL 0,27,190 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL 0,27,195 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL 0,27,194 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL 0,30,167 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL 0,27,191 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL 0,27,176 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL 0,30,189 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=21;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,175 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.1.out /<>/test/mpileup/mpileup.1.out.new [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL 0,27,189 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL 0,27,188 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL 0,24,189 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL 0,24,178 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL 0,27,170 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL 0,30,190 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL 0,27,192 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL 0,27,190 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL 0,27,195 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL 0,27,194 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL 0,30,167 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL 0,27,191 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL 0,27,176 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL 0,30,189 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=21;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,175 0,3,60 0,21,162 etc. .. failed ... test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -b /tmp/9wKauGSdk3/mpileup.bam.list --no-version | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.1.out /<>/test/mpileup/mpileup.1.out.new [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL 0,27,189 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL 0,27,188 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL 0,24,189 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL 0,24,178 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL 0,27,170 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL 0,30,190 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL 0,27,192 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL 0,27,190 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL 0,27,195 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL 0,27,194 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL 0,30,167 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL 0,27,191 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL 0,27,176 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL 0,30,189 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=21;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,175 0,3,60 0,21,162 etc. .. failed ... test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/9wKauGSdk3/mpileup.bam.urllist | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.1.out /<>/test/mpileup/mpileup.1.out.new [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL 0,27,189 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL 0,27,188 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL 0,24,189 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL 0,24,178 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL 0,27,170 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL 0,30,190 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL 0,27,192 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL 0,27,190 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL 0,27,195 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL 0,27,194 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL 0,30,167 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL 0,27,191 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL 0,27,176 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL 0,30,189 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=21;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,175 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.1.out /<>/test/mpileup/mpileup.1.out.new [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL 0,27,189 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL 0,27,188 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL 0,24,189 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL 0,24,178 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL 0,27,170 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL 0,30,190 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL 0,27,192 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL 0,27,190 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL 0,27,195 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL 0,27,194 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL 0,30,167 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL 0,27,191 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL 0,27,176 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL 0,30,189 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=21;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,175 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.1.out /<>/test/mpileup/mpileup.1.out.new [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL 0,27,189 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL 0,27,188 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL 0,24,189 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL 0,24,178 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL 0,27,170 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL 0,30,190 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL 0,27,192 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL 0,27,190 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL 0,27,195 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL 0,27,194 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL 0,30,167 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL 0,27,191 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL 0,27,176 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL 0,30,189 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=21;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,175 0,3,60 0,21,162 etc. .. failed ... test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -b /tmp/9wKauGSdk3/mpileup.cram.list --no-version | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.1.out /<>/test/mpileup/mpileup.1.out.new [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL 0,27,189 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL 0,27,188 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL 0,24,189 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL 0,24,178 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL 0,27,170 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL 0,30,190 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL 0,27,192 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL 0,27,190 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL 0,27,195 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL 0,27,194 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL 0,30,167 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL 0,27,191 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL 0,27,176 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL 0,30,189 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=21;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,175 0,3,60 0,21,162 etc. .. failed ... test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/9wKauGSdk3/mpileup.cram.urllist | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.1.out /<>/test/mpileup/mpileup.1.out.new [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL 0,27,189 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL 0,27,188 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL 0,24,189 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL 0,24,178 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL 0,27,170 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL 0,30,190 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL 0,27,192 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL 0,27,190 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL 0,27,195 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL 0,27,194 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL 0,30,167 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL 0,27,191 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL 0,27,176 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL 0,30,189 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=21;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,183 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL 0,27,175 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.2.out /<>/test/mpileup/mpileup.2.out.new [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 22,54c22,54 < 17 100 . C <*> 0 . DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,189:9:0 0,9,108:3:0 0,15,134:5:0 < 17 101 . C <*> 0 . DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,182:9:0 0,9,99:3:0 0,15,132:5:0 < 17 102 . C <*> 0 . DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,188:9:0 0,9,111:3:0 0,15,139:5:0 < 17 103 . T <*> 0 . DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,189:8:0 0,9,108:3:0 0,15,147:5:0 < 17 104 . G <*> 0 . DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,178:8:0 0,6,89:2:0 0,15,133:5:0 < 17 105 . G <*> 0 . DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,170:9:0 0,9,97:3:0 0,15,125:5:0 < 17 106 . G <*> 0 . DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,190:10:0 0,6,85:2:0 0,15,124:5:0 < 17 107 . C <*> 0 . DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,192:9:0 0,9,108:3:0 0,15,136:5:0 < 17 108 . C <*> 0 . DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,190:9:0 0,9,108:3:0 0,15,135:5:0 < 17 109 . T <*> 0 . DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,195:9:0 0,9,110:3:0 0,15,150:5:0 < 17 110 . G <*> 0 . DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,194:9:0 0,9,104:3:0 0,15,136:5:0 < 17 111 . G <*> 0 . DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,167:10:0 0,6,88:2:0 0,12,118:4:0 < 17 112 . C <*> 0 . DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,191:9:0 0,9,95:3:0 0,15,135:5:0 < 17 113 . A <*> 0 . DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,176:9:0 0,6,87:2:0 0,15,139:5:0 < 17 114 . C <*> 0 . DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,182:9:0 0,9,103:3:0 0,15,133:5:0 < 17 115 . C <*> 0 . DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,189:10:0 0,6,89:2:0 0,18,147:6:0 < 17 116 . A <*> 0 . DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,183:9:0 0,6,90:2:0 0,21,175:7:0 < 17 117 . G <*> 0 . DP=21;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,183:9:0 0,6,85:2:0 0,21,177:7:0 < 17 118 . G <*> 0 . DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,175:9:0 0,3,60:1:0 0,21,162:7:0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.2.out /<>/test/mpileup/mpileup.2.out.new [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 22,54c22,54 < 17 100 . C <*> 0 . DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,189:9:0 0,9,108:3:0 0,15,134:5:0 < 17 101 . C <*> 0 . DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,182:9:0 0,9,99:3:0 0,15,132:5:0 < 17 102 . C <*> 0 . DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,188:9:0 0,9,111:3:0 0,15,139:5:0 < 17 103 . T <*> 0 . DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,189:8:0 0,9,108:3:0 0,15,147:5:0 < 17 104 . G <*> 0 . DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,178:8:0 0,6,89:2:0 0,15,133:5:0 < 17 105 . G <*> 0 . DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,170:9:0 0,9,97:3:0 0,15,125:5:0 < 17 106 . G <*> 0 . DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,190:10:0 0,6,85:2:0 0,15,124:5:0 < 17 107 . C <*> 0 . DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,192:9:0 0,9,108:3:0 0,15,136:5:0 < 17 108 . C <*> 0 . DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,190:9:0 0,9,108:3:0 0,15,135:5:0 < 17 109 . T <*> 0 . DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,195:9:0 0,9,110:3:0 0,15,150:5:0 < 17 110 . G <*> 0 . DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,194:9:0 0,9,104:3:0 0,15,136:5:0 < 17 111 . G <*> 0 . DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,167:10:0 0,6,88:2:0 0,12,118:4:0 < 17 112 . C <*> 0 . DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,191:9:0 0,9,95:3:0 0,15,135:5:0 < 17 113 . A <*> 0 . DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,176:9:0 0,6,87:2:0 0,15,139:5:0 < 17 114 . C <*> 0 . DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,182:9:0 0,9,103:3:0 0,15,133:5:0 < 17 115 . C <*> 0 . DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,189:10:0 0,6,89:2:0 0,18,147:6:0 < 17 116 . A <*> 0 . DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,183:9:0 0,6,90:2:0 0,21,175:7:0 < 17 117 . G <*> 0 . DP=21;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,183:9:0 0,6,85:2:0 0,21,177:7:0 < 17 118 . G <*> 0 . DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,175:9:0 0,3,60:1:0 0,21,162:7:0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.2.out /<>/test/mpileup/mpileup.2.out.new [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 22,54c22,54 < 17 100 . C <*> 0 . DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,189:9:0 0,9,108:3:0 0,15,134:5:0 < 17 101 . C <*> 0 . DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,182:9:0 0,9,99:3:0 0,15,132:5:0 < 17 102 . C <*> 0 . DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,188:9:0 0,9,111:3:0 0,15,139:5:0 < 17 103 . T <*> 0 . DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,189:8:0 0,9,108:3:0 0,15,147:5:0 < 17 104 . G <*> 0 . DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,178:8:0 0,6,89:2:0 0,15,133:5:0 < 17 105 . G <*> 0 . DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,170:9:0 0,9,97:3:0 0,15,125:5:0 < 17 106 . G <*> 0 . DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,190:10:0 0,6,85:2:0 0,15,124:5:0 < 17 107 . C <*> 0 . DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,192:9:0 0,9,108:3:0 0,15,136:5:0 < 17 108 . C <*> 0 . DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,190:9:0 0,9,108:3:0 0,15,135:5:0 < 17 109 . T <*> 0 . DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,195:9:0 0,9,110:3:0 0,15,150:5:0 < 17 110 . G <*> 0 . DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,194:9:0 0,9,104:3:0 0,15,136:5:0 < 17 111 . G <*> 0 . DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,167:10:0 0,6,88:2:0 0,12,118:4:0 < 17 112 . C <*> 0 . DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,191:9:0 0,9,95:3:0 0,15,135:5:0 < 17 113 . A <*> 0 . DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,176:9:0 0,6,87:2:0 0,15,139:5:0 < 17 114 . C <*> 0 . DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,182:9:0 0,9,103:3:0 0,15,133:5:0 < 17 115 . C <*> 0 . DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,189:10:0 0,6,89:2:0 0,18,147:6:0 < 17 116 . A <*> 0 . DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,183:9:0 0,6,90:2:0 0,21,175:7:0 < 17 117 . G <*> 0 . DP=21;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,183:9:0 0,6,85:2:0 0,21,177:7:0 < 17 118 . G <*> 0 . DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,175:9:0 0,3,60:1:0 0,21,162:7:0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.2.out /<>/test/mpileup/mpileup.2.out.new [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 22,54c22,54 < 17 100 . C <*> 0 . DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,189:9:0 0,9,108:3:0 0,15,134:5:0 < 17 101 . C <*> 0 . DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,182:9:0 0,9,99:3:0 0,15,132:5:0 < 17 102 . C <*> 0 . DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,188:9:0 0,9,111:3:0 0,15,139:5:0 < 17 103 . T <*> 0 . DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,189:8:0 0,9,108:3:0 0,15,147:5:0 < 17 104 . G <*> 0 . DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,178:8:0 0,6,89:2:0 0,15,133:5:0 < 17 105 . G <*> 0 . DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,170:9:0 0,9,97:3:0 0,15,125:5:0 < 17 106 . G <*> 0 . DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,190:10:0 0,6,85:2:0 0,15,124:5:0 < 17 107 . C <*> 0 . DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,192:9:0 0,9,108:3:0 0,15,136:5:0 < 17 108 . C <*> 0 . DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,190:9:0 0,9,108:3:0 0,15,135:5:0 < 17 109 . T <*> 0 . DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,195:9:0 0,9,110:3:0 0,15,150:5:0 < 17 110 . G <*> 0 . DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,194:9:0 0,9,104:3:0 0,15,136:5:0 < 17 111 . G <*> 0 . DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,167:10:0 0,6,88:2:0 0,12,118:4:0 < 17 112 . C <*> 0 . DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,191:9:0 0,9,95:3:0 0,15,135:5:0 < 17 113 . A <*> 0 . DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,176:9:0 0,6,87:2:0 0,15,139:5:0 < 17 114 . C <*> 0 . DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,182:9:0 0,9,103:3:0 0,15,133:5:0 < 17 115 . C <*> 0 . DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,189:10:0 0,6,89:2:0 0,18,147:6:0 < 17 116 . A <*> 0 . DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,183:9:0 0,6,90:2:0 0,21,175:7:0 < 17 117 . G <*> 0 . DP=21;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,183:9:0 0,6,85:2:0 0,21,177:7:0 < 17 118 . G <*> 0 . DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,175:9:0 0,3,60:1:0 0,21,162:7:0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.4.out /<>/test/mpileup/mpileup.4.out.new [warning] tag DPR functional, but deprecated. Please switch to `AD` in future. [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [warning] tag DP4 functional, but deprecated. Please switch to `ADF` and `ADR` in future. [warning] tag INFO/DPR functional, but deprecated. Please switch to `INFO/AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 26,58c26,58 < 17 100 . C <*> 0 . DP=18;DPR=17,0;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,189:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,134:5:0:0:5,0,0,0:5,0 < 17 101 . C <*> 0 . DP=18;DPR=17,0;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,182:9:0:0:9,0,0,0:9,0 0,9,99:3:0:0:3,0,0,0:3,0 0,15,132:5:0:0:5,0,0,0:5,0 < 17 102 . C <*> 0 . DP=18;DPR=17,0;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,188:9:0:0:9,0,0,0:9,0 0,9,111:3:0:0:3,0,0,0:3,0 0,15,139:5:0:0:5,0,0,0:5,0 < 17 103 . T <*> 0 . DP=18;DPR=16,0;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,189:8:0:0:8,0,0,0:8,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,147:5:0:0:5,0,0,0:5,0 < 17 104 . G <*> 0 . DP=18;DPR=15,0;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,178:8:0:0:8,0,0,0:8,0 0,6,89:2:0:0:2,0,0,0:2,0 0,15,133:5:0:0:5,0,0,0:5,0 < 17 105 . G <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,170:9:0:0:9,0,0,0:9,0 0,9,97:3:0:0:3,0,0,0:3,0 0,15,125:5:0:0:5,0,0,0:5,0 < 17 106 . G <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,190:10:0:0:10,0,0,0:10,0 0,6,85:2:0:0:2,0,0,0:2,0 0,15,124:5:0:0:5,0,0,0:5,0 < 17 107 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,192:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,136:5:0:0:5,0,0,0:5,0 < 17 108 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,190:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,135:5:0:0:5,0,0,0:5,0 < 17 109 . T <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,195:9:0:0:9,0,0,0:9,0 0,9,110:3:0:0:3,0,0,0:3,0 0,15,150:5:0:0:5,0,0,0:5,0 < 17 110 . G <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,194:9:0:0:9,0,0,0:9,0 0,9,104:3:0:0:3,0,0,0:3,0 0,15,136:5:0:0:5,0,0,0:5,0 < 17 111 . G <*> 0 . DP=19;DPR=16,0;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,167:10:0:0:10,0,0,0:10,0 0,6,88:2:0:0:2,0,0,0:2,0 0,12,118:4:0:0:4,0,0,0:4,0 < 17 112 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,191:9:0:0:9,0,0,0:9,0 0,9,95:3:0:0:3,0,0,0:3,0 0,15,135:5:0:0:5,0,0,0:5,0 < 17 113 . A <*> 0 . DP=19;DPR=16,0;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,176:9:0:0:9,0,0,0:9,0 0,6,87:2:0:0:2,0,0,0:2,0 0,15,139:5:0:0:5,0,0,0:5,0 < 17 114 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,182:9:0:0:9,0,0,0:9,0 0,9,103:3:0:0:3,0,0,0:3,0 0,15,133:5:0:0:5,0,0,0:5,0 < 17 115 . C <*> 0 . DP=21;DPR=18,0;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,189:10:0:0:10,0,0,0:10,0 0,6,89:2:0:0:2,0,0,0:2,0 0,18,147:6:0:0:6,0,0,0:6,0 < 17 116 . A <*> 0 . DP=21;DPR=18,0;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,183:9:0:0:9,0,0,0:9,0 0,6,90:2:0:0:2,0,0,0:2,0 0,21,175:7:0:0:6,1,0,0:7,0 < 17 117 . G <*> 0 . DP=21;DPR=18,0;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,183:9:0:0:9,0,0,0:9,0 0,6,85:2:0:0:2,0,0,0:2,0 0,21,177:7:0:0:6,1,0,0:7,0 < 17 118 . G <*> 0 . DP=20;DPR=17,0;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,175:9:0:0:9,0,0,0:9,0 0,3,60:1:0:0:1,0,0,0:1,0 0,21,162:7:0:0:6,1,0,0:7,0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.4.out /<>/test/mpileup/mpileup.4.out.new [warning] tag DPR functional, but deprecated. Please switch to `AD` in future. [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [warning] tag DP4 functional, but deprecated. Please switch to `ADF` and `ADR` in future. [warning] tag INFO/DPR functional, but deprecated. Please switch to `INFO/AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 26,58c26,58 < 17 100 . C <*> 0 . DP=18;DPR=17,0;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,189:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,134:5:0:0:5,0,0,0:5,0 < 17 101 . C <*> 0 . DP=18;DPR=17,0;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,182:9:0:0:9,0,0,0:9,0 0,9,99:3:0:0:3,0,0,0:3,0 0,15,132:5:0:0:5,0,0,0:5,0 < 17 102 . C <*> 0 . DP=18;DPR=17,0;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,188:9:0:0:9,0,0,0:9,0 0,9,111:3:0:0:3,0,0,0:3,0 0,15,139:5:0:0:5,0,0,0:5,0 < 17 103 . T <*> 0 . DP=18;DPR=16,0;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,189:8:0:0:8,0,0,0:8,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,147:5:0:0:5,0,0,0:5,0 < 17 104 . G <*> 0 . DP=18;DPR=15,0;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,178:8:0:0:8,0,0,0:8,0 0,6,89:2:0:0:2,0,0,0:2,0 0,15,133:5:0:0:5,0,0,0:5,0 < 17 105 . G <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,170:9:0:0:9,0,0,0:9,0 0,9,97:3:0:0:3,0,0,0:3,0 0,15,125:5:0:0:5,0,0,0:5,0 < 17 106 . G <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,190:10:0:0:10,0,0,0:10,0 0,6,85:2:0:0:2,0,0,0:2,0 0,15,124:5:0:0:5,0,0,0:5,0 < 17 107 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,192:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,136:5:0:0:5,0,0,0:5,0 < 17 108 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,190:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,135:5:0:0:5,0,0,0:5,0 < 17 109 . T <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,195:9:0:0:9,0,0,0:9,0 0,9,110:3:0:0:3,0,0,0:3,0 0,15,150:5:0:0:5,0,0,0:5,0 < 17 110 . G <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,194:9:0:0:9,0,0,0:9,0 0,9,104:3:0:0:3,0,0,0:3,0 0,15,136:5:0:0:5,0,0,0:5,0 < 17 111 . G <*> 0 . DP=19;DPR=16,0;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,167:10:0:0:10,0,0,0:10,0 0,6,88:2:0:0:2,0,0,0:2,0 0,12,118:4:0:0:4,0,0,0:4,0 < 17 112 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,191:9:0:0:9,0,0,0:9,0 0,9,95:3:0:0:3,0,0,0:3,0 0,15,135:5:0:0:5,0,0,0:5,0 < 17 113 . A <*> 0 . DP=19;DPR=16,0;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,176:9:0:0:9,0,0,0:9,0 0,6,87:2:0:0:2,0,0,0:2,0 0,15,139:5:0:0:5,0,0,0:5,0 < 17 114 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,182:9:0:0:9,0,0,0:9,0 0,9,103:3:0:0:3,0,0,0:3,0 0,15,133:5:0:0:5,0,0,0:5,0 < 17 115 . C <*> 0 . DP=21;DPR=18,0;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,189:10:0:0:10,0,0,0:10,0 0,6,89:2:0:0:2,0,0,0:2,0 0,18,147:6:0:0:6,0,0,0:6,0 < 17 116 . A <*> 0 . DP=21;DPR=18,0;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,183:9:0:0:9,0,0,0:9,0 0,6,90:2:0:0:2,0,0,0:2,0 0,21,175:7:0:0:6,1,0,0:7,0 < 17 117 . G <*> 0 . DP=21;DPR=18,0;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,183:9:0:0:9,0,0,0:9,0 0,6,85:2:0:0:2,0,0,0:2,0 0,21,177:7:0:0:6,1,0,0:7,0 < 17 118 . G <*> 0 . DP=20;DPR=17,0;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,175:9:0:0:9,0,0,0:9,0 0,3,60:1:0:0:1,0,0,0:1,0 0,21,162:7:0:0:6,1,0,0:7,0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.4.out /<>/test/mpileup/mpileup.4.out.new [warning] tag DPR functional, but deprecated. Please switch to `AD` in future. [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [warning] tag DP4 functional, but deprecated. Please switch to `ADF` and `ADR` in future. [warning] tag INFO/DPR functional, but deprecated. Please switch to `INFO/AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 26,58c26,58 < 17 100 . C <*> 0 . DP=18;DPR=17,0;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,189:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,134:5:0:0:5,0,0,0:5,0 < 17 101 . C <*> 0 . DP=18;DPR=17,0;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,182:9:0:0:9,0,0,0:9,0 0,9,99:3:0:0:3,0,0,0:3,0 0,15,132:5:0:0:5,0,0,0:5,0 < 17 102 . C <*> 0 . DP=18;DPR=17,0;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,188:9:0:0:9,0,0,0:9,0 0,9,111:3:0:0:3,0,0,0:3,0 0,15,139:5:0:0:5,0,0,0:5,0 < 17 103 . T <*> 0 . DP=18;DPR=16,0;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,189:8:0:0:8,0,0,0:8,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,147:5:0:0:5,0,0,0:5,0 < 17 104 . G <*> 0 . DP=18;DPR=15,0;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,178:8:0:0:8,0,0,0:8,0 0,6,89:2:0:0:2,0,0,0:2,0 0,15,133:5:0:0:5,0,0,0:5,0 < 17 105 . G <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,170:9:0:0:9,0,0,0:9,0 0,9,97:3:0:0:3,0,0,0:3,0 0,15,125:5:0:0:5,0,0,0:5,0 < 17 106 . G <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,190:10:0:0:10,0,0,0:10,0 0,6,85:2:0:0:2,0,0,0:2,0 0,15,124:5:0:0:5,0,0,0:5,0 < 17 107 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,192:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,136:5:0:0:5,0,0,0:5,0 < 17 108 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,190:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,135:5:0:0:5,0,0,0:5,0 < 17 109 . T <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,195:9:0:0:9,0,0,0:9,0 0,9,110:3:0:0:3,0,0,0:3,0 0,15,150:5:0:0:5,0,0,0:5,0 < 17 110 . G <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,194:9:0:0:9,0,0,0:9,0 0,9,104:3:0:0:3,0,0,0:3,0 0,15,136:5:0:0:5,0,0,0:5,0 < 17 111 . G <*> 0 . DP=19;DPR=16,0;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,167:10:0:0:10,0,0,0:10,0 0,6,88:2:0:0:2,0,0,0:2,0 0,12,118:4:0:0:4,0,0,0:4,0 < 17 112 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,191:9:0:0:9,0,0,0:9,0 0,9,95:3:0:0:3,0,0,0:3,0 0,15,135:5:0:0:5,0,0,0:5,0 < 17 113 . A <*> 0 . DP=19;DPR=16,0;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,176:9:0:0:9,0,0,0:9,0 0,6,87:2:0:0:2,0,0,0:2,0 0,15,139:5:0:0:5,0,0,0:5,0 < 17 114 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,182:9:0:0:9,0,0,0:9,0 0,9,103:3:0:0:3,0,0,0:3,0 0,15,133:5:0:0:5,0,0,0:5,0 < 17 115 . C <*> 0 . DP=21;DPR=18,0;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,189:10:0:0:10,0,0,0:10,0 0,6,89:2:0:0:2,0,0,0:2,0 0,18,147:6:0:0:6,0,0,0:6,0 < 17 116 . A <*> 0 . DP=21;DPR=18,0;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,183:9:0:0:9,0,0,0:9,0 0,6,90:2:0:0:2,0,0,0:2,0 0,21,175:7:0:0:6,1,0,0:7,0 < 17 117 . G <*> 0 . DP=21;DPR=18,0;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,183:9:0:0:9,0,0,0:9,0 0,6,85:2:0:0:2,0,0,0:2,0 0,21,177:7:0:0:6,1,0,0:7,0 < 17 118 . G <*> 0 . DP=20;DPR=17,0;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,175:9:0:0:9,0,0,0:9,0 0,3,60:1:0:0:1,0,0,0:1,0 0,21,162:7:0:0:6,1,0,0:7,0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.4.out /<>/test/mpileup/mpileup.4.out.new [warning] tag DPR functional, but deprecated. Please switch to `AD` in future. [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [warning] tag DP4 functional, but deprecated. Please switch to `ADF` and `ADR` in future. [warning] tag INFO/DPR functional, but deprecated. Please switch to `INFO/AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 26,58c26,58 < 17 100 . C <*> 0 . DP=18;DPR=17,0;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,189:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,134:5:0:0:5,0,0,0:5,0 < 17 101 . C <*> 0 . DP=18;DPR=17,0;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,182:9:0:0:9,0,0,0:9,0 0,9,99:3:0:0:3,0,0,0:3,0 0,15,132:5:0:0:5,0,0,0:5,0 < 17 102 . C <*> 0 . DP=18;DPR=17,0;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,188:9:0:0:9,0,0,0:9,0 0,9,111:3:0:0:3,0,0,0:3,0 0,15,139:5:0:0:5,0,0,0:5,0 < 17 103 . T <*> 0 . DP=18;DPR=16,0;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,189:8:0:0:8,0,0,0:8,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,147:5:0:0:5,0,0,0:5,0 < 17 104 . G <*> 0 . DP=18;DPR=15,0;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,178:8:0:0:8,0,0,0:8,0 0,6,89:2:0:0:2,0,0,0:2,0 0,15,133:5:0:0:5,0,0,0:5,0 < 17 105 . G <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,170:9:0:0:9,0,0,0:9,0 0,9,97:3:0:0:3,0,0,0:3,0 0,15,125:5:0:0:5,0,0,0:5,0 < 17 106 . G <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,190:10:0:0:10,0,0,0:10,0 0,6,85:2:0:0:2,0,0,0:2,0 0,15,124:5:0:0:5,0,0,0:5,0 < 17 107 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,192:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,136:5:0:0:5,0,0,0:5,0 < 17 108 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,190:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:3,0,0,0:3,0 0,15,135:5:0:0:5,0,0,0:5,0 < 17 109 . T <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,195:9:0:0:9,0,0,0:9,0 0,9,110:3:0:0:3,0,0,0:3,0 0,15,150:5:0:0:5,0,0,0:5,0 < 17 110 . G <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,194:9:0:0:9,0,0,0:9,0 0,9,104:3:0:0:3,0,0,0:3,0 0,15,136:5:0:0:5,0,0,0:5,0 < 17 111 . G <*> 0 . DP=19;DPR=16,0;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,167:10:0:0:10,0,0,0:10,0 0,6,88:2:0:0:2,0,0,0:2,0 0,12,118:4:0:0:4,0,0,0:4,0 < 17 112 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,191:9:0:0:9,0,0,0:9,0 0,9,95:3:0:0:3,0,0,0:3,0 0,15,135:5:0:0:5,0,0,0:5,0 < 17 113 . A <*> 0 . DP=19;DPR=16,0;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,176:9:0:0:9,0,0,0:9,0 0,6,87:2:0:0:2,0,0,0:2,0 0,15,139:5:0:0:5,0,0,0:5,0 < 17 114 . C <*> 0 . DP=19;DPR=17,0;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,182:9:0:0:9,0,0,0:9,0 0,9,103:3:0:0:3,0,0,0:3,0 0,15,133:5:0:0:5,0,0,0:5,0 < 17 115 . C <*> 0 . DP=21;DPR=18,0;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,189:10:0:0:10,0,0,0:10,0 0,6,89:2:0:0:2,0,0,0:2,0 0,18,147:6:0:0:6,0,0,0:6,0 < 17 116 . A <*> 0 . DP=21;DPR=18,0;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,183:9:0:0:9,0,0,0:9,0 0,6,90:2:0:0:2,0,0,0:2,0 0,21,175:7:0:0:6,1,0,0:7,0 < 17 117 . G <*> 0 . DP=21;DPR=18,0;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,183:9:0:0:9,0,0,0:9,0 0,6,85:2:0:0:2,0,0,0:2,0 0,21,177:7:0:0:6,1,0,0:7,0 < 17 118 . G <*> 0 . DP=20;DPR=17,0;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,175:9:0:0:9,0,0,0:9,0 0,3,60:1:0:0:1,0,0,0:1,0 0,21,162:7:0:0:6,1,0,0:7,0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.5.out /<>/test/mpileup/mpileup.5.out.new [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 28,60c28,60 < 17 100 . C <*> 0 . DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,189:9:0:9,0:0,0:9,0 0,9,108:3:0:3,0:0,0:3,0 0,15,134:5:0:5,0:0,0:5,0 < 17 101 . C <*> 0 . DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,182:9:0:9,0:0,0:9,0 0,9,99:3:0:3,0:0,0:3,0 0,15,132:5:0:5,0:0,0:5,0 < 17 102 . C <*> 0 . DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,188:9:0:9,0:0,0:9,0 0,9,111:3:0:3,0:0,0:3,0 0,15,139:5:0:5,0:0,0:5,0 < 17 103 . T <*> 0 . DP=18;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,189:8:0:8,0:0,0:8,0 0,9,108:3:0:3,0:0,0:3,0 0,15,147:5:0:5,0:0,0:5,0 < 17 104 . G <*> 0 . DP=18;ADF=15,0;ADR=0,0;AD=15,0;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,178:8:0:8,0:0,0:8,0 0,6,89:2:0:2,0:0,0:2,0 0,15,133:5:0:5,0:0,0:5,0 < 17 105 . G <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,170:9:0:9,0:0,0:9,0 0,9,97:3:0:3,0:0,0:3,0 0,15,125:5:0:5,0:0,0:5,0 < 17 106 . G <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,190:10:0:10,0:0,0:10,0 0,6,85:2:0:2,0:0,0:2,0 0,15,124:5:0:5,0:0,0:5,0 < 17 107 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,192:9:0:9,0:0,0:9,0 0,9,108:3:0:3,0:0,0:3,0 0,15,136:5:0:5,0:0,0:5,0 < 17 108 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,190:9:0:9,0:0,0:9,0 0,9,108:3:0:3,0:0,0:3,0 0,15,135:5:0:5,0:0,0:5,0 < 17 109 . T <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,195:9:0:9,0:0,0:9,0 0,9,110:3:0:3,0:0,0:3,0 0,15,150:5:0:5,0:0,0:5,0 < 17 110 . G <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,194:9:0:9,0:0,0:9,0 0,9,104:3:0:3,0:0,0:3,0 0,15,136:5:0:5,0:0,0:5,0 < 17 111 . G <*> 0 . DP=19;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,167:10:0:10,0:0,0:10,0 0,6,88:2:0:2,0:0,0:2,0 0,12,118:4:0:4,0:0,0:4,0 < 17 112 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,191:9:0:9,0:0,0:9,0 0,9,95:3:0:3,0:0,0:3,0 0,15,135:5:0:5,0:0,0:5,0 < 17 113 . A <*> 0 . DP=19;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,176:9:0:9,0:0,0:9,0 0,6,87:2:0:2,0:0,0:2,0 0,15,139:5:0:5,0:0,0:5,0 < 17 114 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,182:9:0:9,0:0,0:9,0 0,9,103:3:0:3,0:0,0:3,0 0,15,133:5:0:5,0:0,0:5,0 < 17 115 . C <*> 0 . DP=21;ADF=18,0;ADR=0,0;AD=18,0;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,189:10:0:10,0:0,0:10,0 0,6,89:2:0:2,0:0,0:2,0 0,18,147:6:0:6,0:0,0:6,0 < 17 116 . A <*> 0 . DP=21;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,183:9:0:9,0:0,0:9,0 0,6,90:2:0:2,0:0,0:2,0 0,21,175:7:0:6,0:1,0:7,0 < 17 117 . G <*> 0 . DP=21;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,183:9:0:9,0:0,0:9,0 0,6,85:2:0:2,0:0,0:2,0 0,21,177:7:0:6,0:1,0:7,0 < 17 118 . G <*> 0 . DP=20;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,175:9:0:9,0:0,0:9,0 0,3,60:1:0:1,0:0,0:1,0 0,21,162:7:0:6,0:1,0:7,0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.5.out /<>/test/mpileup/mpileup.5.out.new [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 28,60c28,60 < 17 100 . C <*> 0 . DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,189:9:0:9,0:0,0:9,0 0,9,108:3:0:3,0:0,0:3,0 0,15,134:5:0:5,0:0,0:5,0 < 17 101 . C <*> 0 . DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,182:9:0:9,0:0,0:9,0 0,9,99:3:0:3,0:0,0:3,0 0,15,132:5:0:5,0:0,0:5,0 < 17 102 . C <*> 0 . DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,188:9:0:9,0:0,0:9,0 0,9,111:3:0:3,0:0,0:3,0 0,15,139:5:0:5,0:0,0:5,0 < 17 103 . T <*> 0 . DP=18;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,189:8:0:8,0:0,0:8,0 0,9,108:3:0:3,0:0,0:3,0 0,15,147:5:0:5,0:0,0:5,0 < 17 104 . G <*> 0 . DP=18;ADF=15,0;ADR=0,0;AD=15,0;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,178:8:0:8,0:0,0:8,0 0,6,89:2:0:2,0:0,0:2,0 0,15,133:5:0:5,0:0,0:5,0 < 17 105 . G <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,170:9:0:9,0:0,0:9,0 0,9,97:3:0:3,0:0,0:3,0 0,15,125:5:0:5,0:0,0:5,0 < 17 106 . G <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,190:10:0:10,0:0,0:10,0 0,6,85:2:0:2,0:0,0:2,0 0,15,124:5:0:5,0:0,0:5,0 < 17 107 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,192:9:0:9,0:0,0:9,0 0,9,108:3:0:3,0:0,0:3,0 0,15,136:5:0:5,0:0,0:5,0 < 17 108 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,190:9:0:9,0:0,0:9,0 0,9,108:3:0:3,0:0,0:3,0 0,15,135:5:0:5,0:0,0:5,0 < 17 109 . T <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,195:9:0:9,0:0,0:9,0 0,9,110:3:0:3,0:0,0:3,0 0,15,150:5:0:5,0:0,0:5,0 < 17 110 . G <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,194:9:0:9,0:0,0:9,0 0,9,104:3:0:3,0:0,0:3,0 0,15,136:5:0:5,0:0,0:5,0 < 17 111 . G <*> 0 . DP=19;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,167:10:0:10,0:0,0:10,0 0,6,88:2:0:2,0:0,0:2,0 0,12,118:4:0:4,0:0,0:4,0 < 17 112 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,191:9:0:9,0:0,0:9,0 0,9,95:3:0:3,0:0,0:3,0 0,15,135:5:0:5,0:0,0:5,0 < 17 113 . A <*> 0 . DP=19;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,176:9:0:9,0:0,0:9,0 0,6,87:2:0:2,0:0,0:2,0 0,15,139:5:0:5,0:0,0:5,0 < 17 114 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,182:9:0:9,0:0,0:9,0 0,9,103:3:0:3,0:0,0:3,0 0,15,133:5:0:5,0:0,0:5,0 < 17 115 . C <*> 0 . DP=21;ADF=18,0;ADR=0,0;AD=18,0;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,189:10:0:10,0:0,0:10,0 0,6,89:2:0:2,0:0,0:2,0 0,18,147:6:0:6,0:0,0:6,0 < 17 116 . A <*> 0 . DP=21;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,183:9:0:9,0:0,0:9,0 0,6,90:2:0:2,0:0,0:2,0 0,21,175:7:0:6,0:1,0:7,0 < 17 117 . G <*> 0 . DP=21;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,183:9:0:9,0:0,0:9,0 0,6,85:2:0:2,0:0,0:2,0 0,21,177:7:0:6,0:1,0:7,0 < 17 118 . G <*> 0 . DP=20;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,175:9:0:9,0:0,0:9,0 0,3,60:1:0:1,0:0,0:1,0 0,21,162:7:0:6,0:1,0:7,0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.5.out /<>/test/mpileup/mpileup.5.out.new [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 28,60c28,60 < 17 100 . C <*> 0 . DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,189:9:0:9,0:0,0:9,0 0,9,108:3:0:3,0:0,0:3,0 0,15,134:5:0:5,0:0,0:5,0 < 17 101 . C <*> 0 . DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,182:9:0:9,0:0,0:9,0 0,9,99:3:0:3,0:0,0:3,0 0,15,132:5:0:5,0:0,0:5,0 < 17 102 . C <*> 0 . DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,188:9:0:9,0:0,0:9,0 0,9,111:3:0:3,0:0,0:3,0 0,15,139:5:0:5,0:0,0:5,0 < 17 103 . T <*> 0 . DP=18;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,189:8:0:8,0:0,0:8,0 0,9,108:3:0:3,0:0,0:3,0 0,15,147:5:0:5,0:0,0:5,0 < 17 104 . G <*> 0 . DP=18;ADF=15,0;ADR=0,0;AD=15,0;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,178:8:0:8,0:0,0:8,0 0,6,89:2:0:2,0:0,0:2,0 0,15,133:5:0:5,0:0,0:5,0 < 17 105 . G <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,170:9:0:9,0:0,0:9,0 0,9,97:3:0:3,0:0,0:3,0 0,15,125:5:0:5,0:0,0:5,0 < 17 106 . G <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,190:10:0:10,0:0,0:10,0 0,6,85:2:0:2,0:0,0:2,0 0,15,124:5:0:5,0:0,0:5,0 < 17 107 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,192:9:0:9,0:0,0:9,0 0,9,108:3:0:3,0:0,0:3,0 0,15,136:5:0:5,0:0,0:5,0 < 17 108 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,190:9:0:9,0:0,0:9,0 0,9,108:3:0:3,0:0,0:3,0 0,15,135:5:0:5,0:0,0:5,0 < 17 109 . T <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,195:9:0:9,0:0,0:9,0 0,9,110:3:0:3,0:0,0:3,0 0,15,150:5:0:5,0:0,0:5,0 < 17 110 . G <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,194:9:0:9,0:0,0:9,0 0,9,104:3:0:3,0:0,0:3,0 0,15,136:5:0:5,0:0,0:5,0 < 17 111 . G <*> 0 . DP=19;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,167:10:0:10,0:0,0:10,0 0,6,88:2:0:2,0:0,0:2,0 0,12,118:4:0:4,0:0,0:4,0 < 17 112 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,191:9:0:9,0:0,0:9,0 0,9,95:3:0:3,0:0,0:3,0 0,15,135:5:0:5,0:0,0:5,0 < 17 113 . A <*> 0 . DP=19;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,176:9:0:9,0:0,0:9,0 0,6,87:2:0:2,0:0,0:2,0 0,15,139:5:0:5,0:0,0:5,0 < 17 114 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,182:9:0:9,0:0,0:9,0 0,9,103:3:0:3,0:0,0:3,0 0,15,133:5:0:5,0:0,0:5,0 < 17 115 . C <*> 0 . DP=21;ADF=18,0;ADR=0,0;AD=18,0;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,189:10:0:10,0:0,0:10,0 0,6,89:2:0:2,0:0,0:2,0 0,18,147:6:0:6,0:0,0:6,0 < 17 116 . A <*> 0 . DP=21;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,183:9:0:9,0:0,0:9,0 0,6,90:2:0:2,0:0,0:2,0 0,21,175:7:0:6,0:1,0:7,0 < 17 117 . G <*> 0 . DP=21;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,183:9:0:9,0:0,0:9,0 0,6,85:2:0:2,0:0,0:2,0 0,21,177:7:0:6,0:1,0:7,0 < 17 118 . G <*> 0 . DP=20;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,175:9:0:9,0:0,0:9,0 0,3,60:1:0:1,0:0,0:1,0 0,21,162:7:0:6,0:1,0:7,0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.5.out /<>/test/mpileup/mpileup.5.out.new [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 28,60c28,60 < 17 100 . C <*> 0 . DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,189:9:0:9,0:0,0:9,0 0,9,108:3:0:3,0:0,0:3,0 0,15,134:5:0:5,0:0,0:5,0 < 17 101 . C <*> 0 . DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,182:9:0:9,0:0,0:9,0 0,9,99:3:0:3,0:0,0:3,0 0,15,132:5:0:5,0:0,0:5,0 < 17 102 . C <*> 0 . DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,188:9:0:9,0:0,0:9,0 0,9,111:3:0:3,0:0,0:3,0 0,15,139:5:0:5,0:0,0:5,0 < 17 103 . T <*> 0 . DP=18;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,189:8:0:8,0:0,0:8,0 0,9,108:3:0:3,0:0,0:3,0 0,15,147:5:0:5,0:0,0:5,0 < 17 104 . G <*> 0 . DP=18;ADF=15,0;ADR=0,0;AD=15,0;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,178:8:0:8,0:0,0:8,0 0,6,89:2:0:2,0:0,0:2,0 0,15,133:5:0:5,0:0,0:5,0 < 17 105 . G <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,170:9:0:9,0:0,0:9,0 0,9,97:3:0:3,0:0,0:3,0 0,15,125:5:0:5,0:0,0:5,0 < 17 106 . G <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,190:10:0:10,0:0,0:10,0 0,6,85:2:0:2,0:0,0:2,0 0,15,124:5:0:5,0:0,0:5,0 < 17 107 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,192:9:0:9,0:0,0:9,0 0,9,108:3:0:3,0:0,0:3,0 0,15,136:5:0:5,0:0,0:5,0 < 17 108 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,190:9:0:9,0:0,0:9,0 0,9,108:3:0:3,0:0,0:3,0 0,15,135:5:0:5,0:0,0:5,0 < 17 109 . T <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,195:9:0:9,0:0,0:9,0 0,9,110:3:0:3,0:0,0:3,0 0,15,150:5:0:5,0:0,0:5,0 < 17 110 . G <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,194:9:0:9,0:0,0:9,0 0,9,104:3:0:3,0:0,0:3,0 0,15,136:5:0:5,0:0,0:5,0 < 17 111 . G <*> 0 . DP=19;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,167:10:0:10,0:0,0:10,0 0,6,88:2:0:2,0:0,0:2,0 0,12,118:4:0:4,0:0,0:4,0 < 17 112 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,191:9:0:9,0:0,0:9,0 0,9,95:3:0:3,0:0,0:3,0 0,15,135:5:0:5,0:0,0:5,0 < 17 113 . A <*> 0 . DP=19;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,176:9:0:9,0:0,0:9,0 0,6,87:2:0:2,0:0,0:2,0 0,15,139:5:0:5,0:0,0:5,0 < 17 114 . C <*> 0 . DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,182:9:0:9,0:0,0:9,0 0,9,103:3:0:3,0:0,0:3,0 0,15,133:5:0:5,0:0,0:5,0 < 17 115 . C <*> 0 . DP=21;ADF=18,0;ADR=0,0;AD=18,0;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,189:10:0:10,0:0,0:10,0 0,6,89:2:0:2,0:0,0:2,0 0,18,147:6:0:6,0:0,0:6,0 < 17 116 . A <*> 0 . DP=21;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,183:9:0:9,0:0,0:9,0 0,6,90:2:0:2,0:0,0:2,0 0,21,175:7:0:6,0:1,0:7,0 < 17 117 . G <*> 0 . DP=21;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,183:9:0:9,0:0,0:9,0 0,6,85:2:0:2,0:0,0:2,0 0,21,177:7:0:6,0:1,0:7,0 < 17 118 . G <*> 0 . DP=20;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,175:9:0:9,0:0,0:9,0 0,3,60:1:0:1,0:0,0:1,0 0,21,162:7:0:6,0:1,0:7,0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 24c24 < 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,85:2 0,12,118:4 --- > 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,91:2 0,12,118:4 26c26 < 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,73:2 0,12,97:4 --- > 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,75:2 0,12,97:4 46,47c46,47 < 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,90:2 0,21,221:7 < 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,131:5 0,24,221:8 --- > 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,97:2 0,21,221:7 > 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,146:5 0,24,221:8 .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 24c24 < 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,85:2 0,12,118:4 --- > 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,91:2 0,12,118:4 26c26 < 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,73:2 0,12,97:4 --- > 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,75:2 0,12,97:4 46,47c46,47 < 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,90:2 0,21,221:7 < 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,131:5 0,24,221:8 --- > 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,97:2 0,21,221:7 > 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,146:5 0,24,221:8 .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 24c24 < 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,85:2 0,12,118:4 --- > 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,91:2 0,12,118:4 26c26 < 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,73:2 0,12,97:4 --- > 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,75:2 0,12,97:4 46,47c46,47 < 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,90:2 0,21,221:7 < 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,131:5 0,24,221:8 --- > 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,97:2 0,21,221:7 > 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,146:5 0,24,221:8 .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 24c24 < 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,85:2 0,12,118:4 --- > 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,91:2 0,12,118:4 26c26 < 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,73:2 0,12,97:4 --- > 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,75:2 0,12,97:4 46,47c46,47 < 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,90:2 0,21,221:7 < 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,131:5 0,24,221:8 --- > 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,97:2 0,21,221:7 > 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,146:5 0,24,221:8 .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 24c24 < 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,85:2 0,12,118:4 --- > 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,91:2 0,12,118:4 26c26 < 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,73:2 0,12,97:4 --- > 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,75:2 0,12,97:4 46,47c46,47 < 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,90:2 0,21,221:7 < 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,131:5 0,24,221:8 --- > 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,97:2 0,21,221:7 > 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,146:5 0,24,221:8 .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 24c24 < 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,85:2 0,12,118:4 --- > 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,91:2 0,12,118:4 26c26 < 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,73:2 0,12,97:4 --- > 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,75:2 0,12,97:4 46,47c46,47 < 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,90:2 0,21,221:7 < 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,131:5 0,24,221:8 --- > 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,97:2 0,21,221:7 > 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,146:5 0,24,221:8 .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 24c24 < 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,85:2 0,12,118:4 --- > 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,91:2 0,12,118:4 26c26 < 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,73:2 0,12,97:4 --- > 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,75:2 0,12,97:4 46,47c46,47 < 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,90:2 0,21,221:7 < 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,131:5 0,24,221:8 --- > 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,97:2 0,21,221:7 > 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,146:5 0,24,221:8 .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new [warning] tag DV functional, but deprecated. Please switch to `AD` in future. [mpileup] 3 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 24c24 < 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,85:2 0,12,118:4 --- > 17 100 . C <*> . . END=117;MinDP=2;QS=3,0 PL:DP 0,24,178:8 0,6,91:2 0,12,118:4 26c26 < 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,73:2 0,12,97:4 --- > 17 119 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,75:2 0,12,97:4 46,47c46,47 < 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,90:2 0,21,221:7 < 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,131:5 0,24,221:8 --- > 17 413 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,42,255:14 0,6,97:2 0,21,221:7 > 17 465 . C <*> . . END=511;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,146:5 0,24,221:8 .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.7.out /<>/test/mpileup/mpileup.7.out.new [mpileup] 2 samples in 2 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0 PL 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0 PL 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0 PL 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0 PL 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0 PL 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0 PL 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0 PL 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0 PL 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.7.out /<>/test/mpileup/mpileup.7.out.new [mpileup] 2 samples in 2 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0 PL 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0 PL 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0 PL 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0 PL 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0 PL 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0 PL 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0 PL 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0 PL 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.7.out /<>/test/mpileup/mpileup.7.out.new [mpileup] 2 samples in 2 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0 PL 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0 PL 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0 PL 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0 PL 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0 PL 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0 PL 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0 PL 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0 PL 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.7.out /<>/test/mpileup/mpileup.7.out.new [mpileup] 2 samples in 2 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0 PL 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0 PL 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0 PL 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0 PL 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0 PL 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0 PL 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0 PL 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0 PL 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.7.out /<>/test/mpileup/mpileup.7.out.new [mpileup] 2 samples in 2 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0 PL 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0 PL 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0 PL 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0 PL 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0 PL 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0 PL 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0 PL 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0 PL 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.7.out /<>/test/mpileup/mpileup.7.out.new [mpileup] 2 samples in 2 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0 PL 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0 PL 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0 PL 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0 PL 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0 PL 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0 PL 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0 PL 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0 PL 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.7.out /<>/test/mpileup/mpileup.7.out.new [mpileup] 2 samples in 2 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0 PL 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0 PL 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0 PL 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0 PL 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0 PL 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0 PL 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0 PL 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0 PL 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.7.out /<>/test/mpileup/mpileup.7.out.new [mpileup] 2 samples in 2 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0 PL 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0 PL 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0 PL 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0 PL 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0 PL 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0 PL 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0 PL 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0 PL 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.9.out /<>/test/mpileup/mpileup.9.out.new [mpileup] 2 samples in 2 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0 PL 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0 PL 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0 PL 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0 PL 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0 PL 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0 PL 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0 PL 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0 PL 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.9.out /<>/test/mpileup/mpileup.9.out.new [mpileup] 2 samples in 2 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0 PL 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0 PL 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0 PL 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0 PL 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0 PL 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0 PL 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0 PL 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0 PL 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.9.out /<>/test/mpileup/mpileup.9.out.new [mpileup] 2 samples in 2 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0 PL 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0 PL 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0 PL 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0 PL 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0 PL 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0 PL 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0 PL 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0 PL 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.9.out /<>/test/mpileup/mpileup.9.out.new [mpileup] 2 samples in 2 input files [mpileup] maximum number of reads per input file set to -d 250 20,52c20,52 < 17 100 . C <*> 0 . DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0 PL 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0 PL 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0 PL 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0 PL 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0 PL 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0 PL 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0 PL 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0 PL 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0 PL 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0 PL 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0 PL 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.10.out /<>/test/mpileup/mpileup.10.out.new [mpileup] 5 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 Note: The maximum per-sample depth with -d 250 is 150.0x 20,52c20,52 < 17 100 . C <*> 0 . DP=16;I16=15,0,0,0,609,26637,0,0,838,48482,0,0,310,7132,0,0;QS=5,0;MQ0F=0 PL 0,3,19 0,6,78 0,12,128 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=16;I16=15,0,0,0,587,25433,0,0,838,48482,0,0,309,7011,0,0;QS=5,0;MQ0F=0 PL 0,3,22 0,6,79 0,12,123 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=16;I16=15,0,0,0,621,27715,0,0,838,48482,0,0,308,6904,0,0;QS=5,0;MQ0F=0 PL 0,3,20 0,6,78 0,12,129 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=16;I16=14,0,0,0,612,28790,0,0,809,47641,0,0,301,6775,0,0;QS=4,0;MQ0F=0 PL 0,0,0 0,6,79 0,12,131 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=16;I16=13,0,0,0,546,24526,0,0,780,46800,0,0,273,6009,0,0;QS=4,0;MQ0F=0 PL 0,0,0 0,6,78 0,12,123 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=17;I16=15,0,0,0,542,21886,0,0,869,51241,0,0,295,6507,0,0;QS=5,0;MQ0F=0 PL 0,3,26 0,6,77 0,12,106 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=17;I16=15,0,0,0,570,23834,0,0,869,51241,0,0,277,5851,0,0;QS=5,0;MQ0F=0 PL 0,6,43 0,6,75 0,12,130 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=17;I16=15,0,0,0,614,26864,0,0,869,51241,0,0,291,6299,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,77 0,12,130 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=17;I16=15,0,0,0,615,27183,0,0,869,51241,0,0,288,6170,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,78 0,12,128 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=17;I16=15,0,0,0,664,31304,0,0,869,51241,0,0,285,6059,0,0;QS=5,0;MQ0F=0 PL 0,3,33 0,6,77 0,12,133 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=17;I16=15,0,0,0,624,28074,0,0,869,51241,0,0,282,5966,0,0;QS=5,0;MQ0F=0 PL 0,3,35 0,6,78 0,12,130 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=17;I16=14,0,0,0,514,21894,0,0,809,47641,0,0,250,5124,0,0;QS=5,0;MQ0F=0 PL 0,6,45 0,6,75 0,12,92 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=17;I16=15,0,0,0,600,26654,0,0,869,51241,0,0,274,5738,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,77 0,12,129 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=17;I16=14,0,0,0,575,25583,0,0,840,50400,0,0,244,4978,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,71 0,12,120 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=17;I16=15,0,0,0,595,25667,0,0,869,51241,0,0,264,5486,0,0;QS=5,0;MQ0F=0 PL 0,3,33 0,6,75 0,12,118 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=19;I16=16,0,0,0,635,27881,0,0,929,54841,0,0,252,5086,0,0;QS=5,0;MQ0F=0 PL 0,6,43 0,6,80 0,12,123 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=19;I16=15,1,0,0,653,29009,0,0,929,54841,0,0,231,4637,0,0;QS=5,0;MQSB=1;MQ0F=0 PL 0,3,37 0,6,75 0,12,121 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=19;I16=15,1,0,0,642,27956,0,0,929,54841,0,0,227,4535,0,0;QS=5,0;MQSB=1;MQ0F=0 PL 0,3,37 0,6,77 0,12,117 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=19;I16=15,1,0,0,599,25205,0,0,898,52082,0,0,243,4897,0,0;QS=5,0;MQSB=1;MQ0F=0 PL 0,6,43 0,6,77 0,12,116 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.10.out /<>/test/mpileup/mpileup.10.out.new [mpileup] 5 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 Note: The maximum per-sample depth with -d 250 is 150.0x 20,52c20,52 < 17 100 . C <*> 0 . DP=16;I16=15,0,0,0,609,26637,0,0,838,48482,0,0,310,7132,0,0;QS=5,0;MQ0F=0 PL 0,3,19 0,6,78 0,12,128 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=16;I16=15,0,0,0,587,25433,0,0,838,48482,0,0,309,7011,0,0;QS=5,0;MQ0F=0 PL 0,3,22 0,6,79 0,12,123 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=16;I16=15,0,0,0,621,27715,0,0,838,48482,0,0,308,6904,0,0;QS=5,0;MQ0F=0 PL 0,3,20 0,6,78 0,12,129 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=16;I16=14,0,0,0,612,28790,0,0,809,47641,0,0,301,6775,0,0;QS=4,0;MQ0F=0 PL 0,0,0 0,6,79 0,12,131 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=16;I16=13,0,0,0,546,24526,0,0,780,46800,0,0,273,6009,0,0;QS=4,0;MQ0F=0 PL 0,0,0 0,6,78 0,12,123 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=17;I16=15,0,0,0,542,21886,0,0,869,51241,0,0,295,6507,0,0;QS=5,0;MQ0F=0 PL 0,3,26 0,6,77 0,12,106 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=17;I16=15,0,0,0,570,23834,0,0,869,51241,0,0,277,5851,0,0;QS=5,0;MQ0F=0 PL 0,6,43 0,6,75 0,12,130 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=17;I16=15,0,0,0,614,26864,0,0,869,51241,0,0,291,6299,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,77 0,12,130 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=17;I16=15,0,0,0,615,27183,0,0,869,51241,0,0,288,6170,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,78 0,12,128 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=17;I16=15,0,0,0,664,31304,0,0,869,51241,0,0,285,6059,0,0;QS=5,0;MQ0F=0 PL 0,3,33 0,6,77 0,12,133 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=17;I16=15,0,0,0,624,28074,0,0,869,51241,0,0,282,5966,0,0;QS=5,0;MQ0F=0 PL 0,3,35 0,6,78 0,12,130 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=17;I16=14,0,0,0,514,21894,0,0,809,47641,0,0,250,5124,0,0;QS=5,0;MQ0F=0 PL 0,6,45 0,6,75 0,12,92 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=17;I16=15,0,0,0,600,26654,0,0,869,51241,0,0,274,5738,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,77 0,12,129 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=17;I16=14,0,0,0,575,25583,0,0,840,50400,0,0,244,4978,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,71 0,12,120 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=17;I16=15,0,0,0,595,25667,0,0,869,51241,0,0,264,5486,0,0;QS=5,0;MQ0F=0 PL 0,3,33 0,6,75 0,12,118 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=19;I16=16,0,0,0,635,27881,0,0,929,54841,0,0,252,5086,0,0;QS=5,0;MQ0F=0 PL 0,6,43 0,6,80 0,12,123 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=19;I16=15,1,0,0,653,29009,0,0,929,54841,0,0,231,4637,0,0;QS=5,0;MQSB=1;MQ0F=0 PL 0,3,37 0,6,75 0,12,121 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=19;I16=15,1,0,0,642,27956,0,0,929,54841,0,0,227,4535,0,0;QS=5,0;MQSB=1;MQ0F=0 PL 0,3,37 0,6,77 0,12,117 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=19;I16=15,1,0,0,599,25205,0,0,898,52082,0,0,243,4897,0,0;QS=5,0;MQSB=1;MQ0F=0 PL 0,6,43 0,6,77 0,12,116 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.10.out /<>/test/mpileup/mpileup.10.out.new [mpileup] 5 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 Note: The maximum per-sample depth with -d 250 is 150.0x 20,52c20,52 < 17 100 . C <*> 0 . DP=16;I16=15,0,0,0,609,26637,0,0,838,48482,0,0,310,7132,0,0;QS=5,0;MQ0F=0 PL 0,3,19 0,6,78 0,12,128 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=16;I16=15,0,0,0,587,25433,0,0,838,48482,0,0,309,7011,0,0;QS=5,0;MQ0F=0 PL 0,3,22 0,6,79 0,12,123 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=16;I16=15,0,0,0,621,27715,0,0,838,48482,0,0,308,6904,0,0;QS=5,0;MQ0F=0 PL 0,3,20 0,6,78 0,12,129 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=16;I16=14,0,0,0,612,28790,0,0,809,47641,0,0,301,6775,0,0;QS=4,0;MQ0F=0 PL 0,0,0 0,6,79 0,12,131 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=16;I16=13,0,0,0,546,24526,0,0,780,46800,0,0,273,6009,0,0;QS=4,0;MQ0F=0 PL 0,0,0 0,6,78 0,12,123 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=17;I16=15,0,0,0,542,21886,0,0,869,51241,0,0,295,6507,0,0;QS=5,0;MQ0F=0 PL 0,3,26 0,6,77 0,12,106 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=17;I16=15,0,0,0,570,23834,0,0,869,51241,0,0,277,5851,0,0;QS=5,0;MQ0F=0 PL 0,6,43 0,6,75 0,12,130 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=17;I16=15,0,0,0,614,26864,0,0,869,51241,0,0,291,6299,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,77 0,12,130 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=17;I16=15,0,0,0,615,27183,0,0,869,51241,0,0,288,6170,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,78 0,12,128 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=17;I16=15,0,0,0,664,31304,0,0,869,51241,0,0,285,6059,0,0;QS=5,0;MQ0F=0 PL 0,3,33 0,6,77 0,12,133 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=17;I16=15,0,0,0,624,28074,0,0,869,51241,0,0,282,5966,0,0;QS=5,0;MQ0F=0 PL 0,3,35 0,6,78 0,12,130 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=17;I16=14,0,0,0,514,21894,0,0,809,47641,0,0,250,5124,0,0;QS=5,0;MQ0F=0 PL 0,6,45 0,6,75 0,12,92 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=17;I16=15,0,0,0,600,26654,0,0,869,51241,0,0,274,5738,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,77 0,12,129 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=17;I16=14,0,0,0,575,25583,0,0,840,50400,0,0,244,4978,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,71 0,12,120 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=17;I16=15,0,0,0,595,25667,0,0,869,51241,0,0,264,5486,0,0;QS=5,0;MQ0F=0 PL 0,3,33 0,6,75 0,12,118 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=19;I16=16,0,0,0,635,27881,0,0,929,54841,0,0,252,5086,0,0;QS=5,0;MQ0F=0 PL 0,6,43 0,6,80 0,12,123 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=19;I16=15,1,0,0,653,29009,0,0,929,54841,0,0,231,4637,0,0;QS=5,0;MQSB=1;MQ0F=0 PL 0,3,37 0,6,75 0,12,121 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=19;I16=15,1,0,0,642,27956,0,0,929,54841,0,0,227,4535,0,0;QS=5,0;MQSB=1;MQ0F=0 PL 0,3,37 0,6,77 0,12,117 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=19;I16=15,1,0,0,599,25205,0,0,898,52082,0,0,243,4897,0,0;QS=5,0;MQSB=1;MQ0F=0 PL 0,6,43 0,6,77 0,12,116 0,3,60 0,21,162 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.10.out /<>/test/mpileup/mpileup.10.out.new [mpileup] 5 samples in 3 input files [mpileup] maximum number of reads per input file set to -d 250 Note: The maximum per-sample depth with -d 250 is 150.0x 20,52c20,52 < 17 100 . C <*> 0 . DP=16;I16=15,0,0,0,609,26637,0,0,838,48482,0,0,310,7132,0,0;QS=5,0;MQ0F=0 PL 0,3,19 0,6,78 0,12,128 0,9,108 0,15,134 < 17 101 . C <*> 0 . DP=16;I16=15,0,0,0,587,25433,0,0,838,48482,0,0,309,7011,0,0;QS=5,0;MQ0F=0 PL 0,3,22 0,6,79 0,12,123 0,9,99 0,15,132 < 17 102 . C <*> 0 . DP=16;I16=15,0,0,0,621,27715,0,0,838,48482,0,0,308,6904,0,0;QS=5,0;MQ0F=0 PL 0,3,20 0,6,78 0,12,129 0,9,111 0,15,139 < 17 103 . T <*> 0 . DP=16;I16=14,0,0,0,612,28790,0,0,809,47641,0,0,301,6775,0,0;QS=4,0;MQ0F=0 PL 0,0,0 0,6,79 0,12,131 0,9,108 0,15,147 < 17 104 . G <*> 0 . DP=16;I16=13,0,0,0,546,24526,0,0,780,46800,0,0,273,6009,0,0;QS=4,0;MQ0F=0 PL 0,0,0 0,6,78 0,12,123 0,6,89 0,15,133 < 17 105 . G <*> 0 . DP=17;I16=15,0,0,0,542,21886,0,0,869,51241,0,0,295,6507,0,0;QS=5,0;MQ0F=0 PL 0,3,26 0,6,77 0,12,106 0,9,97 0,15,125 < 17 106 . G <*> 0 . DP=17;I16=15,0,0,0,570,23834,0,0,869,51241,0,0,277,5851,0,0;QS=5,0;MQ0F=0 PL 0,6,43 0,6,75 0,12,130 0,6,85 0,15,124 < 17 107 . C <*> 0 . DP=17;I16=15,0,0,0,614,26864,0,0,869,51241,0,0,291,6299,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,77 0,12,130 0,9,108 0,15,136 < 17 108 . C <*> 0 . DP=17;I16=15,0,0,0,615,27183,0,0,869,51241,0,0,288,6170,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,78 0,12,128 0,9,108 0,15,135 < 17 109 . T <*> 0 . DP=17;I16=15,0,0,0,664,31304,0,0,869,51241,0,0,285,6059,0,0;QS=5,0;MQ0F=0 PL 0,3,33 0,6,77 0,12,133 0,9,110 0,15,150 < 17 110 . G <*> 0 . DP=17;I16=15,0,0,0,624,28074,0,0,869,51241,0,0,282,5966,0,0;QS=5,0;MQ0F=0 PL 0,3,35 0,6,78 0,12,130 0,9,104 0,15,136 < 17 111 . G <*> 0 . DP=17;I16=14,0,0,0,514,21894,0,0,809,47641,0,0,250,5124,0,0;QS=5,0;MQ0F=0 PL 0,6,45 0,6,75 0,12,92 0,6,88 0,12,118 < 17 112 . C <*> 0 . DP=17;I16=15,0,0,0,600,26654,0,0,869,51241,0,0,274,5738,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,77 0,12,129 0,9,95 0,15,135 < 17 113 . A <*> 0 . DP=17;I16=14,0,0,0,575,25583,0,0,840,50400,0,0,244,4978,0,0;QS=5,0;MQ0F=0 PL 0,3,30 0,6,71 0,12,120 0,6,87 0,15,139 < 17 114 . C <*> 0 . DP=17;I16=15,0,0,0,595,25667,0,0,869,51241,0,0,264,5486,0,0;QS=5,0;MQ0F=0 PL 0,3,33 0,6,75 0,12,118 0,9,103 0,15,133 < 17 115 . C <*> 0 . DP=19;I16=16,0,0,0,635,27881,0,0,929,54841,0,0,252,5086,0,0;QS=5,0;MQ0F=0 PL 0,6,43 0,6,80 0,12,123 0,6,89 0,18,147 < 17 116 . A <*> 0 . DP=19;I16=15,1,0,0,653,29009,0,0,929,54841,0,0,231,4637,0,0;QS=5,0;MQSB=1;MQ0F=0 PL 0,3,37 0,6,75 0,12,121 0,6,90 0,21,175 < 17 117 . G <*> 0 . DP=19;I16=15,1,0,0,642,27956,0,0,929,54841,0,0,227,4535,0,0;QS=5,0;MQSB=1;MQ0F=0 PL 0,3,37 0,6,77 0,12,117 0,6,85 0,21,177 < 17 118 . G <*> 0 . DP=19;I16=15,1,0,0,599,25205,0,0,898,52082,0,0,243,4897,0,0;QS=5,0;MQSB=1;MQ0F=0 PL 0,6,43 0,6,77 0,12,116 0,3,60 0,21,162 etc. .. failed ... test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 1138,1162c1138,1162 < 17 1118 . T <*> 0 . DP=12;I16=10,1,0,0,471,21403,0,0,660,39600,0,0,233,5335,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,248 < 17 1119 . C <*> 0 . DP=12;I16=10,1,0,0,480,22008,0,0,660,39600,0,0,233,5293,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1120 . C <*> 0 . DP=12;I16=10,1,0,0,479,22119,0,0,660,39600,0,0,233,5263,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,33,255 < 17 1121 . A <*> 0 . DP=13;I16=11,1,0,0,515,23435,0,0,720,43200,0,0,233,5245,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1122 . T <*> 0 . DP=13;I16=11,1,0,0,517,23663,0,0,720,43200,0,0,233,5189,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1123 . T <*> 0 . DP=13;I16=11,1,0,0,521,24255,0,0,720,43200,0,0,233,5145,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1124 . A <*> 0 . DP=13;I16=11,1,0,0,514,23562,0,0,720,43200,0,0,233,5113,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1125 . T <*> 0 . DP=13;I16=11,1,0,0,527,24853,0,0,720,43200,0,0,233,5093,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1126 . C <*> 0 . DP=13;I16=11,1,0,0,527,24651,0,0,720,43200,0,0,233,5085,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1127 . T <*> 0 . DP=13;I16=11,1,0,0,541,26591,0,0,720,43200,0,0,233,5089,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1128 . G <*> 0 . DP=13;I16=11,1,0,0,525,24825,0,0,720,43200,0,0,233,5105,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1129 . A G,<*> 0 . DP=13;I16=11,0,0,1,482,22610,32,1024,660,39600,60,3600,207,4457,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,4,198,33,201,219 < 17 1130 . A <*> 0 . DP=13;I16=11,1,0,0,525,24437,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1131 . A <*> 0 . DP=13;I16=11,1,0,0,520,23980,0,0,720,43200,0,0,230,5066,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1132 . T <*> 0 . DP=13;I16=11,1,0,0,524,24784,0,0,720,43200,0,0,229,5073,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1133 . G <*> 0 . DP=13;I16=11,1,0,0,524,24346,0,0,720,43200,0,0,228,5090,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1134 . C <*> 0 . DP=13;I16=11,1,0,0,536,25356,0,0,720,43200,0,0,227,5117,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1135 . T <*> 0 . DP=13;I16=11,1,0,0,563,28333,0,0,720,43200,0,0,226,5154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 < 17 1136 . T <*> 0 . DP=13;I16=11,1,0,0,521,24617,0,0,720,43200,0,0,225,5201,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,36,255 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/indel-AD.1.out /<>/test/mpileup/indel-AD.1.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 81,224c81,225 < 000000F 451 . T <*> 0 . DP=43;I16=25,14,0,0,1491,58519,0,0,2340,140400,0,0,708,15882,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,117,255:39,0 < 000000F 452 . G <*> 0 . DP=45;I16=26,14,0,0,1555,62549,0,0,2400,144000,0,0,731,16465,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,120,255:40,0 < 000000F 453 . C <*> 0 . DP=45;I16=25,14,0,0,1608,69148,0,0,2340,140400,0,0,731,16555,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,117,255:39,0 < 000000F 454 . A <*> 0 . DP=47;I16=26,17,0,0,1722,73004,0,0,2580,154800,0,0,817,18519,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,129,255:43,0 < 000000F 455 . G <*> 0 . DP=48;I16=27,17,0,0,1837,80653,0,0,2640,158400,0,0,861,19597,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,132,255:44,0 < 000000F 456 . T <*> 0 . DP=49;I16=25,19,0,0,1769,75479,0,0,2640,158400,0,0,853,19595,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,132,255:44,0 < 000000F 457 . T <*> 0 . DP=49;I16=28,19,0,0,1876,79136,0,0,2820,169200,0,0,905,20453,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,141,255:47,0 < 000000F 458 . A <*> 0 . DP=50;I16=26,19,0,0,1833,79049,0,0,2700,162000,0,0,884,20032,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,135,255:45,0 < 000000F 459 . G <*> 0 . DP=50;I16=27,19,0,0,1837,78191,0,0,2760,165600,0,0,907,20581,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,138,255:46,0 < 000000F 460 . A <*> 0 . DP=49;I16=26,16,0,0,1625,66133,0,0,2520,151200,0,0,842,19170,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,126,255:42,0 < 000000F 461 . A <*> 0 . DP=52;I16=26,15,0,0,1591,64163,0,0,2460,147600,0,0,854,19910,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,123,255:41,0 < 000000F 462 . A <*> 0 . DP=52;I16=25,19,0,0,1675,67071,0,0,2640,158400,0,0,920,21276,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,132,255:44,0 < 000000F 463 . A <*> 0 . DP=52;I16=27,19,0,0,1807,73217,0,0,2760,165600,0,0,966,22322,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,138,255:46,0 < 000000F 464 . T <*> 0 . DP=52;I16=27,21,0,0,1925,81581,0,0,2880,172800,0,0,1008,23194,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,144,255:48,0 < 000000F 465 . A <*> 0 . DP=52;I16=28,21,0,0,1986,84592,0,0,2940,176400,0,0,1050,24328,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,148,255:49,0 < 000000F 466 . A <*> 0 . DP=52;I16=26,19,0,0,1845,79017,0,0,2700,162000,0,0,983,22855,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,135,255:45,0 < 000000F 467 . T <*> 0 . DP=53;I16=27,20,0,0,1882,79994,0,0,2820,169200,0,0,1006,23366,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,141,255:47,0 < 000000F 468 . A <*> 0 . DP=54;I16=27,22,0,0,1975,84097,0,0,2940,176400,0,0,1053,24625,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,148,255:49,0 < 000000F 469 . T <*> 0 . DP=54;I16=28,22,0,0,2066,89308,0,0,3000,180000,0,0,1096,25728,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,151,255:50,0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/indel-AD.1.out /<>/test/mpileup/indel-AD.1.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 81,224c81,225 < 000000F 451 . T <*> 0 . DP=43;I16=25,14,0,0,1491,58519,0,0,2340,140400,0,0,708,15882,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,117,255:39,0 < 000000F 452 . G <*> 0 . DP=45;I16=26,14,0,0,1555,62549,0,0,2400,144000,0,0,731,16465,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,120,255:40,0 < 000000F 453 . C <*> 0 . DP=45;I16=25,14,0,0,1608,69148,0,0,2340,140400,0,0,731,16555,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,117,255:39,0 < 000000F 454 . A <*> 0 . DP=47;I16=26,17,0,0,1722,73004,0,0,2580,154800,0,0,817,18519,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,129,255:43,0 < 000000F 455 . G <*> 0 . DP=48;I16=27,17,0,0,1837,80653,0,0,2640,158400,0,0,861,19597,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,132,255:44,0 < 000000F 456 . T <*> 0 . DP=49;I16=25,19,0,0,1769,75479,0,0,2640,158400,0,0,853,19595,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,132,255:44,0 < 000000F 457 . T <*> 0 . DP=49;I16=28,19,0,0,1876,79136,0,0,2820,169200,0,0,905,20453,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,141,255:47,0 < 000000F 458 . A <*> 0 . DP=50;I16=26,19,0,0,1833,79049,0,0,2700,162000,0,0,884,20032,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,135,255:45,0 < 000000F 459 . G <*> 0 . DP=50;I16=27,19,0,0,1837,78191,0,0,2760,165600,0,0,907,20581,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,138,255:46,0 < 000000F 460 . A <*> 0 . DP=49;I16=26,16,0,0,1625,66133,0,0,2520,151200,0,0,842,19170,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,126,255:42,0 < 000000F 461 . A <*> 0 . DP=52;I16=26,15,0,0,1591,64163,0,0,2460,147600,0,0,854,19910,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,123,255:41,0 < 000000F 462 . A <*> 0 . DP=52;I16=25,19,0,0,1675,67071,0,0,2640,158400,0,0,920,21276,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,132,255:44,0 < 000000F 463 . A <*> 0 . DP=52;I16=27,19,0,0,1807,73217,0,0,2760,165600,0,0,966,22322,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,138,255:46,0 < 000000F 464 . T <*> 0 . DP=52;I16=27,21,0,0,1925,81581,0,0,2880,172800,0,0,1008,23194,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,144,255:48,0 < 000000F 465 . A <*> 0 . DP=52;I16=28,21,0,0,1986,84592,0,0,2940,176400,0,0,1050,24328,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,148,255:49,0 < 000000F 466 . A <*> 0 . DP=52;I16=26,19,0,0,1845,79017,0,0,2700,162000,0,0,983,22855,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,135,255:45,0 < 000000F 467 . T <*> 0 . DP=53;I16=27,20,0,0,1882,79994,0,0,2820,169200,0,0,1006,23366,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,141,255:47,0 < 000000F 468 . A <*> 0 . DP=54;I16=27,22,0,0,1975,84097,0,0,2940,176400,0,0,1053,24625,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,148,255:49,0 < 000000F 469 . T <*> 0 . DP=54;I16=28,22,0,0,2066,89308,0,0,3000,180000,0,0,1096,25728,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,151,255:50,0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/indel-AD.1.out /<>/test/mpileup/indel-AD.1.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 81,224c81,225 < 000000F 451 . T <*> 0 . DP=43;I16=25,14,0,0,1491,58519,0,0,2340,140400,0,0,708,15882,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,117,255:39,0 < 000000F 452 . G <*> 0 . DP=45;I16=26,14,0,0,1555,62549,0,0,2400,144000,0,0,731,16465,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,120,255:40,0 < 000000F 453 . C <*> 0 . DP=45;I16=25,14,0,0,1608,69148,0,0,2340,140400,0,0,731,16555,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,117,255:39,0 < 000000F 454 . A <*> 0 . DP=47;I16=26,17,0,0,1722,73004,0,0,2580,154800,0,0,817,18519,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,129,255:43,0 < 000000F 455 . G <*> 0 . DP=48;I16=27,17,0,0,1837,80653,0,0,2640,158400,0,0,861,19597,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,132,255:44,0 < 000000F 456 . T <*> 0 . DP=49;I16=25,19,0,0,1769,75479,0,0,2640,158400,0,0,853,19595,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,132,255:44,0 < 000000F 457 . T <*> 0 . DP=49;I16=28,19,0,0,1876,79136,0,0,2820,169200,0,0,905,20453,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,141,255:47,0 < 000000F 458 . A <*> 0 . DP=50;I16=26,19,0,0,1833,79049,0,0,2700,162000,0,0,884,20032,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,135,255:45,0 < 000000F 459 . G <*> 0 . DP=50;I16=27,19,0,0,1837,78191,0,0,2760,165600,0,0,907,20581,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,138,255:46,0 < 000000F 460 . A <*> 0 . DP=49;I16=26,16,0,0,1625,66133,0,0,2520,151200,0,0,842,19170,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,126,255:42,0 < 000000F 461 . A <*> 0 . DP=52;I16=26,15,0,0,1591,64163,0,0,2460,147600,0,0,854,19910,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,123,255:41,0 < 000000F 462 . A <*> 0 . DP=52;I16=25,19,0,0,1675,67071,0,0,2640,158400,0,0,920,21276,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,132,255:44,0 < 000000F 463 . A <*> 0 . DP=52;I16=27,19,0,0,1807,73217,0,0,2760,165600,0,0,966,22322,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,138,255:46,0 < 000000F 464 . T <*> 0 . DP=52;I16=27,21,0,0,1925,81581,0,0,2880,172800,0,0,1008,23194,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,144,255:48,0 < 000000F 465 . A <*> 0 . DP=52;I16=28,21,0,0,1986,84592,0,0,2940,176400,0,0,1050,24328,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,148,255:49,0 < 000000F 466 . A <*> 0 . DP=52;I16=26,19,0,0,1845,79017,0,0,2700,162000,0,0,983,22855,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,135,255:45,0 < 000000F 467 . T <*> 0 . DP=53;I16=27,20,0,0,1882,79994,0,0,2820,169200,0,0,1006,23366,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,141,255:47,0 < 000000F 468 . A <*> 0 . DP=54;I16=27,22,0,0,1975,84097,0,0,2940,176400,0,0,1053,24625,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,148,255:49,0 < 000000F 469 . T <*> 0 . DP=54;I16=28,22,0,0,2066,89308,0,0,3000,180000,0,0,1096,25728,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,151,255:50,0 etc. .. failed ... 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 The outputs differ: /<>/test/mpileup/indel-AD.1.out /<>/test/mpileup/indel-AD.1.out.new [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 81,224c81,225 < 000000F 451 . T <*> 0 . DP=43;I16=25,14,0,0,1491,58519,0,0,2340,140400,0,0,708,15882,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,117,255:39,0 < 000000F 452 . G <*> 0 . DP=45;I16=26,14,0,0,1555,62549,0,0,2400,144000,0,0,731,16465,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,120,255:40,0 < 000000F 453 . C <*> 0 . DP=45;I16=25,14,0,0,1608,69148,0,0,2340,140400,0,0,731,16555,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,117,255:39,0 < 000000F 454 . A <*> 0 . DP=47;I16=26,17,0,0,1722,73004,0,0,2580,154800,0,0,817,18519,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,129,255:43,0 < 000000F 455 . G <*> 0 . DP=48;I16=27,17,0,0,1837,80653,0,0,2640,158400,0,0,861,19597,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,132,255:44,0 < 000000F 456 . T <*> 0 . DP=49;I16=25,19,0,0,1769,75479,0,0,2640,158400,0,0,853,19595,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,132,255:44,0 < 000000F 457 . T <*> 0 . DP=49;I16=28,19,0,0,1876,79136,0,0,2820,169200,0,0,905,20453,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,141,255:47,0 < 000000F 458 . A <*> 0 . DP=50;I16=26,19,0,0,1833,79049,0,0,2700,162000,0,0,884,20032,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,135,255:45,0 < 000000F 459 . G <*> 0 . DP=50;I16=27,19,0,0,1837,78191,0,0,2760,165600,0,0,907,20581,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,138,255:46,0 < 000000F 460 . A <*> 0 . DP=49;I16=26,16,0,0,1625,66133,0,0,2520,151200,0,0,842,19170,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,126,255:42,0 < 000000F 461 . A <*> 0 . DP=52;I16=26,15,0,0,1591,64163,0,0,2460,147600,0,0,854,19910,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,123,255:41,0 < 000000F 462 . A <*> 0 . DP=52;I16=25,19,0,0,1675,67071,0,0,2640,158400,0,0,920,21276,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,132,255:44,0 < 000000F 463 . A <*> 0 . DP=52;I16=27,19,0,0,1807,73217,0,0,2760,165600,0,0,966,22322,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,138,255:46,0 < 000000F 464 . T <*> 0 . DP=52;I16=27,21,0,0,1925,81581,0,0,2880,172800,0,0,1008,23194,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,144,255:48,0 < 000000F 465 . A <*> 0 . DP=52;I16=28,21,0,0,1986,84592,0,0,2940,176400,0,0,1050,24328,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,148,255:49,0 < 000000F 466 . A <*> 0 . DP=52;I16=26,19,0,0,1845,79017,0,0,2700,162000,0,0,983,22855,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,135,255:45,0 < 000000F 467 . T <*> 0 . DP=53;I16=27,20,0,0,1882,79994,0,0,2820,169200,0,0,1006,23366,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,141,255:47,0 < 000000F 468 . A <*> 0 . DP=54;I16=27,22,0,0,1975,84097,0,0,2940,176400,0,0,1053,24625,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,148,255:49,0 < 000000F 469 . T <*> 0 . DP=54;I16=28,22,0,0,2066,89308,0,0,3000,180000,0,0,1096,25728,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,151,255:50,0 etc. .. failed ... 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/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/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/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/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/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/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/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/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/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/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/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: 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: 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: /<>/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/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/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/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/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/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/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/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/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/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/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/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/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: 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/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 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/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/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/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/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/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/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/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/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/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-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/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-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-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/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/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/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/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-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/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/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/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/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: 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: /<>/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 -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/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/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/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/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/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/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/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: /<>/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: cd /<>/test/csq/EMN908947 && /<>/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../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/EMN908947 && /<>/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../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/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: /<>/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/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/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/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_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -Or -G30 --AF-file /<>/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -Or -G30 --AF-file /<>/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 /tmp/9wKauGSdk3/gtcheck.1.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,GT /tmp/9wKauGSdk3/gtcheck.1.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,PL /tmp/9wKauGSdk3/gtcheck.1.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,GT /tmp/9wKauGSdk3/gtcheck.1.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,PL /tmp/9wKauGSdk3/gtcheck.1.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -p s1,s1 /tmp/9wKauGSdk3/gtcheck.1.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 /tmp/9wKauGSdk3/gtcheck.2.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 /tmp/9wKauGSdk3/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/9wKauGSdk3/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -P /<>/test/gtcheck.3.pairs /tmp/9wKauGSdk3/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL /tmp/9wKauGSdk3/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 --n-matches 4 /tmp/9wKauGSdk3/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/9wKauGSdk3/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/9wKauGSdk3/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/9wKauGSdk3/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/9wKauGSdk3/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/9wKauGSdk3/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -p B,C,B,D /tmp/9wKauGSdk3/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,GT -H /tmp/9wKauGSdk3/gtcheck.1.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,PL -H /tmp/9wKauGSdk3/gtcheck.1.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,GT -H /tmp/9wKauGSdk3/gtcheck.1.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,PL -H /tmp/9wKauGSdk3/gtcheck.1.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -P /<>/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/9wKauGSdk3/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -P /<>/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/9wKauGSdk3/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 30 /tmp/9wKauGSdk3/gtcheck.1.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/9wKauGSdk3/gtcheck.1.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 300 /tmp/9wKauGSdk3/gtcheck.1.vcf.gz -g /tmp/9wKauGSdk3/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u PL -e 30 /tmp/9wKauGSdk3/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1210 passed .. 1142 failed .. 68 make[2]: *** [Makefile:297: test-no-plugins] Error 1 make[2]: Leaving directory '/<>' make[1]: *** [debian/rules:47: override_dh_auto_test] Error 2 make[1]: Leaving directory '/<>' make: *** [debian/rules:11: binary-arch] Error 2 dpkg-buildpackage.pl: error: debian/rules binary-arch subprocess returned exit status 2 === USAGE-SUMMARY BEGIN === SUMMARY: host: bos02-arm64-010; CPUs: 4/4; CPU avg: 52%; CPU max: 100%; base memory: 0.2 GB; peak memory: 0.4 GB; total memory: 7.8 GB SUMMARY: swap peak/total: 0.0/0.0 GB; disk start/end/total: 2.8/2.8/58.0 GB; disk delta: 0.0 GB === USAGE-SUMMARY END === -------------------------------------------------------------------------------- Build finished at 2021-10-05T21:56:44Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: n/a Build-Time: 95 Distribution: impish Fail-Stage: build Host Architecture: armhf Install-Time: 17 Job: bcftools_1.11-1.dsc Machine Architecture: arm64 Package: bcftools Package-Time: 114 Source-Version: 1.11-1 Space: n/a Status: attempted Version: 1.11-1 -------------------------------------------------------------------------------- Finished at 2021-10-05T21:56:44Z Build needed 00:01:54, no disk space E: Build failure (dpkg-buildpackage died) Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=impish --arch=armhf PACKAGEBUILD-22121190 Scanning for processes to kill in build PACKAGEBUILD-22121190