[med-svn] [bcftools] 01/01: Keep logs of failed architectures to enable comparison with latest patch
Andreas Tille
tille at debian.org
Thu Dec 14 15:22:24 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch logs
in repository bcftools.
commit d90ed1428529c422583a919d7ba084d591552694
Author: Andreas Tille <tille at debian.org>
Date: Wed Dec 13 16:24:30 2017 +0100
Keep logs of failed architectures to enable comparison with latest patch
---
bcftools_1.6-1_alpha.log | 4090 ++++++++++++++++++++++++++++++++++
bcftools_1.6-1_i386.log | 4289 ++++++++++++++++++++++++++++++++++++
bcftools_1.6-1_kfreebsd-i386.log | 4294 ++++++++++++++++++++++++++++++++++++
bcftools_1.6-1_mips.log | 4528 +++++++++++++++++++++++++++++++++++++
bcftools_1.6-1_ppc64.log | 4515 +++++++++++++++++++++++++++++++++++++
bcftools_1.6-1_s390x.log | 4530 ++++++++++++++++++++++++++++++++++++++
bcftools_1.6-1_sparc64.log | 4500 +++++++++++++++++++++++++++++++++++++
get_logs | 8 +
8 files changed, 30754 insertions(+)
diff --git a/bcftools_1.6-1_alpha.log b/bcftools_1.6-1_alpha.log
new file mode 100644
index 0000000..b031b73
--- /dev/null
+++ b/bcftools_1.6-1_alpha.log
@@ -0,0 +1,4090 @@
+
+sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on imago.phys.waikato.ac.nz
+
++==============================================================================+
+| bcftools 1.6-1 (alpha) Tue, 12 Dec 2017 03:01:33 +0000 |
++==============================================================================+
+
+Package: bcftools
+Version: 1.6-1
+Source Version: 1.6-1
+Distribution: experimental
+Machine Architecture: alpha
+Host Architecture: alpha
+Build Architecture: alpha
+Build Type: any
+
+I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-experimental-alpha-sbuild-f23a88de-ca28-411b-a00b-5bb9d1802077' with '<<CHROOT>>'
+
++------------------------------------------------------------------------------+
+| Update chroot |
++------------------------------------------------------------------------------+
+
+Get:1 http://localhost:9999/ports sid InRelease [37.1 kB]
+Get:2 http://localhost:9999/ports unreleased InRelease [40.8 kB]
+Get:3 http://localhost:9999/ports experimental InRelease [37.6 kB]
+Get:4 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:5 http://incoming.ports.debian.org/buildd unstable InRelease [40.0 kB]
+Get:6 http://localhost:9999/ports sid/main all Packages [8365 kB]
+Get:7 http://ftp.debian.org/debian unstable InRelease [240 kB]
+Get:8 http://incoming.ports.debian.org/buildd experimental InRelease [40.0 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-experimental InRelease [58.9 kB]
+Get:10 http://localhost:9999/ports sid/main alpha Packages [19.6 MB]
+Get:11 http://incoming.ports.debian.org/buildd unstable/main alpha Packages [146 kB]
+Get:12 http://ftp.debian.org/debian experimental InRelease [107 kB]
+Get:13 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [117 kB]
+Get:14 http://localhost:9999/ports experimental/main all Packages [394 kB]
+Get:15 http://localhost:9999/ports experimental/main alpha Packages [779 kB]
+Get:16 http://incoming.ports.debian.org/buildd experimental/main alpha Packages [25.9 kB]
+Get:17 http://incoming.debian.org/debian-buildd buildd-experimental/main Sources [35.7 kB]
+Get:18 http://ftp.debian.org/debian unstable/main Sources.diff/Index [27.9 kB]
+Get:19 http://ftp.debian.org/debian experimental/main Sources.diff/Index [27.8 kB]
+Get:20 http://ftp.debian.org/debian unstable/main Sources 2017-12-09-0224.55.pdiff [11.8 kB]
+Get:21 http://ftp.debian.org/debian unstable/main Sources 2017-12-09-1506.09.pdiff [27.9 kB]
+Get:22 http://ftp.debian.org/debian unstable/main Sources 2017-12-09-2022.32.pdiff [9984 B]
+Get:23 http://ftp.debian.org/debian unstable/main Sources 2017-12-10-0220.13.pdiff [13.1 kB]
+Get:24 http://ftp.debian.org/debian unstable/main Sources 2017-12-10-0819.55.pdiff [7068 B]
+Get:25 http://ftp.debian.org/debian unstable/main Sources 2017-12-10-1421.01.pdiff [12.2 kB]
+Get:26 http://ftp.debian.org/debian unstable/main Sources 2017-12-10-2020.16.pdiff [11.7 kB]
+Get:27 http://ftp.debian.org/debian unstable/main Sources 2017-12-11-0223.29.pdiff [7018 B]
+Get:28 http://ftp.debian.org/debian unstable/main Sources 2017-12-11-0822.15.pdiff [4013 B]
+Get:29 http://ftp.debian.org/debian unstable/main Sources 2017-12-11-1420.00.pdiff [9374 B]
+Get:30 http://ftp.debian.org/debian unstable/main Sources 2017-12-11-2029.23.pdiff [12.8 kB]
+Get:30 http://ftp.debian.org/debian unstable/main Sources 2017-12-11-2029.23.pdiff [12.8 kB]
+Get:31 http://ftp.debian.org/debian experimental/main Sources 2017-12-09-0224.55.pdiff [1121 B]
+Get:32 http://ftp.debian.org/debian experimental/main Sources 2017-12-09-1506.09.pdiff [7294 B]
+Get:33 http://ftp.debian.org/debian experimental/main Sources 2017-12-09-2022.32.pdiff [2342 B]
+Get:34 http://ftp.debian.org/debian experimental/main Sources 2017-12-10-0220.13.pdiff [9066 B]
+Get:35 http://ftp.debian.org/debian experimental/main Sources 2017-12-10-0819.55.pdiff [888 B]
+Get:36 http://ftp.debian.org/debian experimental/main Sources 2017-12-10-1421.01.pdiff [4367 B]
+Get:37 http://ftp.debian.org/debian experimental/main Sources 2017-12-10-2020.16.pdiff [1795 B]
+Get:38 http://ftp.debian.org/debian experimental/main Sources 2017-12-11-0223.29.pdiff [2110 B]
+Get:39 http://ftp.debian.org/debian experimental/main Sources 2017-12-11-0822.15.pdiff [688 B]
+Get:40 http://ftp.debian.org/debian experimental/main Sources 2017-12-11-1420.00.pdiff [63 B]
+Get:41 http://ftp.debian.org/debian experimental/main Sources 2017-12-11-2029.23.pdiff [3918 B]
+Get:41 http://ftp.debian.org/debian experimental/main Sources 2017-12-11-2029.23.pdiff [3918 B]
+Fetched 30.3 MB in 19s (1588 kB/s)
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Fetch source files |
++------------------------------------------------------------------------------+
+
+
+Check APT
+---------
+
+Checking available source versions...
+
+Download source files with APT
+------------------------------
+
+Reading package lists...
+NOTICE: 'bcftools' packaging is maintained in the 'Git' version control system at:
+https://anonscm.debian.org/git/debian-med/bcftools.git
+Please use:
+git clone https://anonscm.debian.org/git/debian-med/bcftools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 2342 kB of source archives.
+Get:1 http://ftp.debian.org/debian experimental/main bcftools 1.6-1 (dsc) [2110 B]
+Get:2 http://ftp.debian.org/debian experimental/main bcftools 1.6-1 (tar) [2333 kB]
+Get:3 http://ftp.debian.org/debian experimental/main bcftools 1.6-1 (diff) [6088 B]
+Fetched 2342 kB in 3s (612 kB/s)
+Download complete and in download only mode
+I: NOTICE: Log filtering will replace 'build/bcftools-FHCR8U/bcftools-1.6' with '<<PKGBUILDDIR>>'
+I: NOTICE: Log filtering will replace 'build/bcftools-FHCR8U' with '<<BUILDDIR>>'
+
++------------------------------------------------------------------------------+
+| 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 '/<<BUILDDIR>>/resolver-AsVOOh/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:/<<BUILDDIR>>/resolver-AsVOOh/apt_archive ./ InRelease
+Get:2 copy:/<<BUILDDIR>>/resolver-AsVOOh/apt_archive ./ Release [957 B]
+Ign:3 copy:/<<BUILDDIR>>/resolver-AsVOOh/apt_archive ./ Release.gpg
+Get:4 copy:/<<BUILDDIR>>/resolver-AsVOOh/apt_archive ./ Sources [349 B]
+Get:5 copy:/<<BUILDDIR>>/resolver-AsVOOh/apt_archive ./ Packages [432 B]
+Fetched 1738 B in 0s (53.9 kB/s)
+Reading package lists...
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Install core build dependencies (aptitude-based resolver) |
++------------------------------------------------------------------------------+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ ca-certificates libssl1.1 openssl
+Use 'apt autoremove' to remove them.
+The following additional packages will be installed:
+ aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+Suggested packages:
+ aptitude-doc-en | aptitude-doc apt-xapian-index debtags tasksel
+ libcwidget-dev xapian-tools
+Recommended packages:
+ libparse-debianchangelog-perl
+The following NEW packages will be installed:
+ aptitude aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+0 upgraded, 9 newly installed, 0 to remove and 2 not upgraded.
+Need to get 5245 kB of archives.
+After this operation, 21.9 MB of additional disk space will be used.
+Get:1 http://localhost:9999/ports sid/main alpha libxapian30 alpha 1.4.5-1 [1079 kB]
+Get:2 http://localhost:9999/ports sid/main alpha libsqlite3-0 alpha 3.21.0-1 [628 kB]
+Get:3 http://localhost:9999/ports sid/main alpha aptitude-common all 0.8.10-1 [1591 kB]
+Get:4 http://localhost:9999/ports sid/main alpha libboost-system1.62.0 alpha 1.62.0+dfsg-4+b2 [33.0 kB]
+Get:5 http://localhost:9999/ports sid/main alpha libboost-filesystem1.62.0 alpha 1.62.0+dfsg-4+b2 [63.4 kB]
+Get:6 http://localhost:9999/ports sid/main alpha libboost-iostreams1.62.0 alpha 1.62.0+dfsg-4+b2 [51.9 kB]
+Get:7 http://localhost:9999/ports sid/main alpha libsigc++-2.0-0v5 alpha 2.10.0-1 [62.1 kB]
+Get:8 http://localhost:9999/ports sid/main alpha libcwidget3v5 alpha 0.5.17-6 [292 kB]
+Get:9 http://localhost:9999/ports sid/main alpha aptitude alpha 0.8.10-1 [1445 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 5245 kB in 0s (12.1 MB/s)
+Selecting previously unselected package libxapian30:alpha.
+(Reading database ... 14293 files and directories currently installed.)
+Preparing to unpack .../0-libxapian30_1.4.5-1_alpha.deb ...
+Unpacking libxapian30:alpha (1.4.5-1) ...
+Selecting previously unselected package libsqlite3-0:alpha.
+Preparing to unpack .../1-libsqlite3-0_3.21.0-1_alpha.deb ...
+Unpacking libsqlite3-0:alpha (3.21.0-1) ...
+Selecting previously unselected package aptitude-common.
+Preparing to unpack .../2-aptitude-common_0.8.10-1_all.deb ...
+Unpacking aptitude-common (0.8.10-1) ...
+Selecting previously unselected package libboost-system1.62.0:alpha.
+Preparing to unpack .../3-libboost-system1.62.0_1.62.0+dfsg-4+b2_alpha.deb ...
+Unpacking libboost-system1.62.0:alpha (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libboost-filesystem1.62.0:alpha.
+Preparing to unpack .../4-libboost-filesystem1.62.0_1.62.0+dfsg-4+b2_alpha.deb ...
+Unpacking libboost-filesystem1.62.0:alpha (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libboost-iostreams1.62.0:alpha.
+Preparing to unpack .../5-libboost-iostreams1.62.0_1.62.0+dfsg-4+b2_alpha.deb ...
+Unpacking libboost-iostreams1.62.0:alpha (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libsigc++-2.0-0v5:alpha.
+Preparing to unpack .../6-libsigc++-2.0-0v5_2.10.0-1_alpha.deb ...
+Unpacking libsigc++-2.0-0v5:alpha (2.10.0-1) ...
+Selecting previously unselected package libcwidget3v5:alpha.
+Preparing to unpack .../7-libcwidget3v5_0.5.17-6_alpha.deb ...
+Unpacking libcwidget3v5:alpha (0.5.17-6) ...
+Selecting previously unselected package aptitude.
+Preparing to unpack .../8-aptitude_0.8.10-1_alpha.deb ...
+Unpacking aptitude (0.8.10-1) ...
+Setting up libxapian30:alpha (1.4.5-1) ...
+Setting up aptitude-common (0.8.10-1) ...
+Setting up libboost-iostreams1.62.0:alpha (1.62.0+dfsg-4+b2) ...
+Processing triggers for libc-bin (2.25-1) ...
+Setting up libsqlite3-0:alpha (3.21.0-1) ...
+Setting up libsigc++-2.0-0v5:alpha (2.10.0-1) ...
+Setting up libboost-system1.62.0:alpha (1.62.0+dfsg-4+b2) ...
+Setting up libboost-filesystem1.62.0:alpha (1.62.0+dfsg-4+b2) ...
+Setting up libcwidget3v5:alpha (0.5.17-6) ...
+Setting up aptitude (0.8.10-1) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode
+Processing triggers for libc-bin (2.25-1) ...
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-core-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-core-dummy:alpha
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+0 packages upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
+Need to get 852 B of archives. After unpacking 0 B will be used.
+Writing extended state information...
+Get: 1 copy:/<<BUILDDIR>>/resolver-AsVOOh/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
+Fetched 852 B in 0s (0 B/s)
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 14547 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_alpha.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+
++------------------------------------------------------------------------------+
+| Check architectures |
++------------------------------------------------------------------------------+
+
+Arch check ok (alpha included in any)
+
++------------------------------------------------------------------------------+
+| Install package build dependencies |
++------------------------------------------------------------------------------+
+
+
+Setup apt archive
+-----------------
+
+Merged Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+Filtered Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<<BUILDDIR>>/resolver-AsVOOh/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:/<<BUILDDIR>>/resolver-AsVOOh/apt_archive ./ InRelease
+Get:2 copy:/<<BUILDDIR>>/resolver-AsVOOh/apt_archive ./ Release [963 B]
+Ign:3 copy:/<<BUILDDIR>>/resolver-AsVOOh/apt_archive ./ Release.gpg
+Get:4 copy:/<<BUILDDIR>>/resolver-AsVOOh/apt_archive ./ Sources [546 B]
+Get:5 copy:/<<BUILDDIR>>/resolver-AsVOOh/apt_archive ./ Packages [617 B]
+Fetched 2126 B in 0s (68.0 kB/s)
+Reading package lists...
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Install bcftools build dependencies (aptitude-based resolver) |
++------------------------------------------------------------------------------+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+aptitude is already the newest version (0.8.10-1).
+The following packages were automatically installed and are no longer required:
+ ca-certificates libssl1.1 openssl
+Use 'apt autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-bcftools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-bcftool [...]
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libbz2-dev{a} libcroco3{a} libcurl3-gnutls{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu57{a} libio-pty-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} l [...]
+The following packages are RECOMMENDED but will NOT be installed:
+ bzip2-doc curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx-cur publicsuffix shared-mime-info wget xdg-user-dirs
+0 packages upgraded, 55 newly installed, 0 to remove and 2 not upgraded.
+Need to get 25.4 MB of archives. After unpacking 93.2 MB will be used.
+Writing extended state information...
+Get: 1 copy:/<<BUILDDIR>>/resolver-AsVOOh/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [904 B]
+Get: 2 http://localhost:9999/ports sid/main alpha groff-base alpha 1.22.3-9 [1239 kB]
+Get: 3 http://localhost:9999/ports sid/main alpha libbsd0 alpha 0.8.6-3 [96.4 kB]
+Get: 4 http://localhost:9999/ports sid/main alpha libncurses5 alpha 6.0+20171125-1 [104 kB]
+Get: 5 http://localhost:9999/ports sid/main alpha bsdmainutils alpha 9.0.14 [189 kB]
+Get: 6 http://localhost:9999/ports sid/main alpha libpipeline1 alpha 1.5.0-1 [29.8 kB]
+Get: 7 http://localhost:9999/ports sid/main alpha man-db alpha 2.7.6.1-4 [1053 kB]
+Get: 8 http://localhost:9999/ports sid/main alpha libmagic-mgc alpha 1:5.32-1 [225 kB]
+Get: 9 http://localhost:9999/ports sid/main alpha libmagic1 alpha 1:5.32-1 [120 kB]
+Get: 10 http://localhost:9999/ports sid/main alpha file alpha 1:5.32-1 [64.6 kB]
+Get: 11 http://localhost:9999/ports sid/main alpha gettext-base alpha 0.19.8.1-4 [123 kB]
+Get: 12 http://localhost:9999/ports sid/main alpha libkeyutils1 alpha 1.5.9-9.2 [13.0 kB]
+Get: 13 http://localhost:9999/ports sid/main alpha libkrb5support0 alpha 1.15.2-2 [63.8 kB]
+Get: 14 http://localhost:9999/ports sid/main alpha libk5crypto3 alpha 1.15.2-2 [141 kB]
+Get: 15 http://localhost:9999/ports sid/main alpha libkrb5-3 alpha 1.15.2-2 [318 kB]
+Get: 16 http://localhost:9999/ports sid/main alpha libgssapi-krb5-2 alpha 1.15.2-2 [155 kB]
+Get: 17 http://localhost:9999/ports sid/main alpha libsasl2-modules-db alpha 2.1.27~101-g0780600+dfsg-3 [68.9 kB]
+Get: 18 http://localhost:9999/ports sid/main alpha libsasl2-2 alpha 2.1.27~101-g0780600+dfsg-3 [108 kB]
+Get: 19 http://localhost:9999/ports sid/main alpha libldap-common all 2.4.45+dfsg-1 [87.0 kB]
+Get: 20 http://localhost:9999/ports sid/main alpha libldap-2.4-2 alpha 2.4.45+dfsg-1 [219 kB]
+Get: 21 http://localhost:9999/ports sid/main alpha libicu57 alpha 57.1-8 [7769 kB]
+Get: 22 http://localhost:9999/ports sid/main alpha libxml2 alpha 2.9.4+dfsg1-5.1 [698 kB]
+Get: 23 http://localhost:9999/ports sid/main alpha libsigsegv2 alpha 2.11-1 [30.0 kB]
+Get: 24 http://localhost:9999/ports sid/main alpha m4 alpha 1.4.18-1 [204 kB]
+Get: 25 http://localhost:9999/ports sid/main alpha autoconf all 2.69-11 [341 kB]
+Get: 26 http://localhost:9999/ports sid/main alpha autotools-dev all 20161112.1+nmu1 [74.2 kB]
+Get: 27 http://localhost:9999/ports sid/main alpha automake all 1:1.15.1-3 [736 kB]
+Get: 28 http://localhost:9999/ports sid/main alpha autopoint all 0.19.8.1-4 [434 kB]
+Get: 29 http://localhost:9999/ports sid/main alpha libtool all 2.4.6-2 [545 kB]
+Get: 30 http://localhost:9999/ports sid/main alpha dh-autoreconf all 15 [16.2 kB]
+Get: 31 http://localhost:9999/ports sid/main alpha libarchive-zip-perl all 1.59-1 [95.5 kB]
+Get: 32 http://localhost:9999/ports sid/main alpha libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
+Get: 33 http://localhost:9999/ports sid/main alpha libtimedate-perl all 2.3000-2 [42.2 kB]
+Get: 34 http://localhost:9999/ports sid/main alpha dh-strip-nondeterminism all 0.040-1 [11.8 kB]
+Get: 35 http://localhost:9999/ports sid/main alpha libglib2.0-0 alpha 2.54.0-1 [2810 kB]
+Get: 36 http://localhost:9999/ports sid/main alpha libcroco3 alpha 0.6.12-1 [142 kB]
+Get: 37 http://localhost:9999/ports sid/main alpha gettext alpha 0.19.8.1-4 [1320 kB]
+Get: 38 http://localhost:9999/ports sid/main alpha intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get: 39 http://localhost:9999/ports sid/main alpha po-debconf all 1.0.20 [247 kB]
+Get: 40 http://localhost:9999/ports sid/main alpha debhelper all 10.10.9 [975 kB]
+Get: 41 http://localhost:9999/ports sid/main alpha libbz2-dev alpha 1.0.6-8.1 [36.3 kB]
+Get: 42 http://localhost:9999/ports sid/main alpha libnghttp2-14 alpha 1.28.0-1 [85.6 kB]
+Get: 43 http://localhost:9999/ports sid/main alpha libpsl5 alpha 0.19.1-4 [44.9 kB]
+Get: 44 http://localhost:9999/ports sid/main alpha librtmp1 alpha 2.4+20151223.gitfa8646d.1-1 [63.8 kB]
+Get: 45 http://localhost:9999/ports sid/main alpha libssh2-1 alpha 1.8.0-1 [141 kB]
+Get: 46 http://localhost:9999/ports sid/main alpha libcurl3-gnutls alpha 7.57.0-1 [318 kB]
+Get: 47 http://localhost:9999/ports sid/main alpha libgslcblas0 alpha 2.4+dfsg-6 [83.1 kB]
+Get: 48 http://localhost:9999/ports sid/main alpha libgsl23 alpha 2.4+dfsg-6 [828 kB]
+Get: 49 http://localhost:9999/ports sid/main alpha libgsl-dev alpha 2.4+dfsg-6 [1119 kB]
+Get: 50 http://localhost:9999/ports sid/main alpha libhts2 alpha 1.5-6 [335 kB]
+Get: 51 http://localhost:9999/ports sid/main alpha liblzma-dev alpha 5.2.2-1.3 [307 kB]
+Get: 52 http://localhost:9999/ports sid/main alpha tabix alpha 1.5-6 [360 kB]
+Get: 53 http://localhost:9999/ports sid/main alpha libhts-dev alpha 1.5-6 [454 kB]
+Get: 54 http://localhost:9999/ports sid/main alpha libio-pty-perl alpha 1:1.08-1.1+b4 [34.1 kB]
+Get: 55 http://localhost:9999/ports sid/main alpha zlib1g-dev alpha 1:1.2.8.dfsg-5 [214 kB]
+Fetched 25.4 MB in 6s (3721 kB/s)
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package groff-base.
+(Reading database ...
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(Reading database ... 14547 files and directories currently installed.)
+Preparing to unpack .../00-groff-base_1.22.3-9_alpha.deb ...
+Unpacking groff-base (1.22.3-9) ...
+Selecting previously unselected package libbsd0:alpha.
+Preparing to unpack .../01-libbsd0_0.8.6-3_alpha.deb ...
+Unpacking libbsd0:alpha (0.8.6-3) ...
+Selecting previously unselected package libncurses5:alpha.
+Preparing to unpack .../02-libncurses5_6.0+20171125-1_alpha.deb ...
+Unpacking libncurses5:alpha (6.0+20171125-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../03-bsdmainutils_9.0.14_alpha.deb ...
+Unpacking bsdmainutils (9.0.14) ...
+Selecting previously unselected package libpipeline1:alpha.
+Preparing to unpack .../04-libpipeline1_1.5.0-1_alpha.deb ...
+Unpacking libpipeline1:alpha (1.5.0-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../05-man-db_2.7.6.1-4_alpha.deb ...
+Unpacking man-db (2.7.6.1-4) ...
+Selecting previously unselected package libmagic-mgc.
+Preparing to unpack .../06-libmagic-mgc_1%3a5.32-1_alpha.deb ...
+Unpacking libmagic-mgc (1:5.32-1) ...
+Selecting previously unselected package libmagic1:alpha.
+Preparing to unpack .../07-libmagic1_1%3a5.32-1_alpha.deb ...
+Unpacking libmagic1:alpha (1:5.32-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../08-file_1%3a5.32-1_alpha.deb ...
+Unpacking file (1:5.32-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../09-gettext-base_0.19.8.1-4_alpha.deb ...
+Unpacking gettext-base (0.19.8.1-4) ...
+Selecting previously unselected package libkeyutils1:alpha.
+Preparing to unpack .../10-libkeyutils1_1.5.9-9.2_alpha.deb ...
+Unpacking libkeyutils1:alpha (1.5.9-9.2) ...
+Selecting previously unselected package libkrb5support0:alpha.
+Preparing to unpack .../11-libkrb5support0_1.15.2-2_alpha.deb ...
+Unpacking libkrb5support0:alpha (1.15.2-2) ...
+Selecting previously unselected package libk5crypto3:alpha.
+Preparing to unpack .../12-libk5crypto3_1.15.2-2_alpha.deb ...
+Unpacking libk5crypto3:alpha (1.15.2-2) ...
+Selecting previously unselected package libkrb5-3:alpha.
+Preparing to unpack .../13-libkrb5-3_1.15.2-2_alpha.deb ...
+Unpacking libkrb5-3:alpha (1.15.2-2) ...
+Selecting previously unselected package libgssapi-krb5-2:alpha.
+Preparing to unpack .../14-libgssapi-krb5-2_1.15.2-2_alpha.deb ...
+Unpacking libgssapi-krb5-2:alpha (1.15.2-2) ...
+Selecting previously unselected package libsasl2-modules-db:alpha.
+Preparing to unpack .../15-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3_alpha.deb ...
+Unpacking libsasl2-modules-db:alpha (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libsasl2-2:alpha.
+Preparing to unpack .../16-libsasl2-2_2.1.27~101-g0780600+dfsg-3_alpha.deb ...
+Unpacking libsasl2-2:alpha (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libldap-common.
+Preparing to unpack .../17-libldap-common_2.4.45+dfsg-1_all.deb ...
+Unpacking libldap-common (2.4.45+dfsg-1) ...
+Selecting previously unselected package libldap-2.4-2:alpha.
+Preparing to unpack .../18-libldap-2.4-2_2.4.45+dfsg-1_alpha.deb ...
+Unpacking libldap-2.4-2:alpha (2.4.45+dfsg-1) ...
+Selecting previously unselected package libicu57:alpha.
+Preparing to unpack .../19-libicu57_57.1-8_alpha.deb ...
+Unpacking libicu57:alpha (57.1-8) ...
+Selecting previously unselected package libxml2:alpha.
+Preparing to unpack .../20-libxml2_2.9.4+dfsg1-5.1_alpha.deb ...
+Unpacking libxml2:alpha (2.9.4+dfsg1-5.1) ...
+Selecting previously unselected package libsigsegv2:alpha.
+Preparing to unpack .../21-libsigsegv2_2.11-1_alpha.deb ...
+Unpacking libsigsegv2:alpha (2.11-1) ...
+Selecting previously unselected package m4.
+Preparing to unpack .../22-m4_1.4.18-1_alpha.deb ...
+Unpacking m4 (1.4.18-1) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../23-autoconf_2.69-11_all.deb ...
+Unpacking autoconf (2.69-11) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../24-autotools-dev_20161112.1+nmu1_all.deb ...
+Unpacking autotools-dev (20161112.1+nmu1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../25-automake_1%3a1.15.1-3_all.deb ...
+Unpacking automake (1:1.15.1-3) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../26-autopoint_0.19.8.1-4_all.deb ...
+Unpacking autopoint (0.19.8.1-4) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../27-libtool_2.4.6-2_all.deb ...
+Unpacking libtool (2.4.6-2) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../28-dh-autoreconf_15_all.deb ...
+Unpacking dh-autoreconf (15) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../29-libarchive-zip-perl_1.59-1_all.deb ...
+Unpacking libarchive-zip-perl (1.59-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../30-libfile-stripnondeterminism-perl_0.040-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.040-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../31-libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../32-dh-strip-nondeterminism_0.040-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.040-1) ...
+Selecting previously unselected package libglib2.0-0:alpha.
+Preparing to unpack .../33-libglib2.0-0_2.54.0-1_alpha.deb ...
+Unpacking libglib2.0-0:alpha (2.54.0-1) ...
+Selecting previously unselected package libcroco3:alpha.
+Preparing to unpack .../34-libcroco3_0.6.12-1_alpha.deb ...
+Unpacking libcroco3:alpha (0.6.12-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../35-gettext_0.19.8.1-4_alpha.deb ...
+Unpacking gettext (0.19.8.1-4) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../36-intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../37-po-debconf_1.0.20_all.deb ...
+Unpacking po-debconf (1.0.20) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../38-debhelper_10.10.9_all.deb ...
+Unpacking debhelper (10.10.9) ...
+Selecting previously unselected package libbz2-dev:alpha.
+Preparing to unpack .../39-libbz2-dev_1.0.6-8.1_alpha.deb ...
+Unpacking libbz2-dev:alpha (1.0.6-8.1) ...
+Selecting previously unselected package libnghttp2-14:alpha.
+Preparing to unpack .../40-libnghttp2-14_1.28.0-1_alpha.deb ...
+Unpacking libnghttp2-14:alpha (1.28.0-1) ...
+Selecting previously unselected package libpsl5:alpha.
+Preparing to unpack .../41-libpsl5_0.19.1-4_alpha.deb ...
+Unpacking libpsl5:alpha (0.19.1-4) ...
+Selecting previously unselected package librtmp1:alpha.
+Preparing to unpack .../42-librtmp1_2.4+20151223.gitfa8646d.1-1_alpha.deb ...
+Unpacking librtmp1:alpha (2.4+20151223.gitfa8646d.1-1) ...
+Selecting previously unselected package libssh2-1:alpha.
+Preparing to unpack .../43-libssh2-1_1.8.0-1_alpha.deb ...
+Unpacking libssh2-1:alpha (1.8.0-1) ...
+Selecting previously unselected package libcurl3-gnutls:alpha.
+Preparing to unpack .../44-libcurl3-gnutls_7.57.0-1_alpha.deb ...
+Unpacking libcurl3-gnutls:alpha (7.57.0-1) ...
+Selecting previously unselected package libgslcblas0:alpha.
+Preparing to unpack .../45-libgslcblas0_2.4+dfsg-6_alpha.deb ...
+Unpacking libgslcblas0:alpha (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl23:alpha.
+Preparing to unpack .../46-libgsl23_2.4+dfsg-6_alpha.deb ...
+Unpacking libgsl23:alpha (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl-dev.
+Preparing to unpack .../47-libgsl-dev_2.4+dfsg-6_alpha.deb ...
+Unpacking libgsl-dev (2.4+dfsg-6) ...
+Selecting previously unselected package libhts2:alpha.
+Preparing to unpack .../48-libhts2_1.5-6_alpha.deb ...
+Unpacking libhts2:alpha (1.5-6) ...
+Selecting previously unselected package liblzma-dev:alpha.
+Preparing to unpack .../49-liblzma-dev_5.2.2-1.3_alpha.deb ...
+Unpacking liblzma-dev:alpha (5.2.2-1.3) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../50-tabix_1.5-6_alpha.deb ...
+Unpacking tabix (1.5-6) ...
+Selecting previously unselected package libhts-dev:alpha.
+Preparing to unpack .../51-libhts-dev_1.5-6_alpha.deb ...
+Unpacking libhts-dev:alpha (1.5-6) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../52-libio-pty-perl_1%3a1.08-1.1+b4_alpha.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b4) ...
+Selecting previously unselected package zlib1g-dev:alpha.
+Preparing to unpack .../53-zlib1g-dev_1%3a1.2.8.dfsg-5_alpha.deb ...
+Unpacking zlib1g-dev:alpha (1:1.2.8.dfsg-5) ...
+Selecting previously unselected package sbuild-build-depends-bcftools-dummy.
+Preparing to unpack .../54-sbuild-build-depends-bcftools-dummy_0.invalid.0_alpha.deb ...
+Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Setting up libncurses5:alpha (6.0+20171125-1) ...
+Setting up libbz2-dev:alpha (1.0.6-8.1) ...
+Setting up libarchive-zip-perl (1.59-1) ...
+Setting up libnghttp2-14:alpha (1.28.0-1) ...
+Setting up libio-pty-perl (1:1.08-1.1+b4) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libsigsegv2:alpha (2.11-1) ...
+Setting up libldap-common (2.4.45+dfsg-1) ...
+Setting up libpsl5:alpha (0.19.1-4) ...
+Setting up groff-base (1.22.3-9) ...
+Setting up libglib2.0-0:alpha (2.54.0-1) ...
+No schema files found: doing nothing.
+Setting up libsasl2-modules-db:alpha (2.1.27~101-g0780600+dfsg-3) ...
+Setting up libsasl2-2:alpha (2.1.27~101-g0780600+dfsg-3) ...
+Setting up gettext-base (0.19.8.1-4) ...
+Setting up libpipeline1:alpha (1.5.0-1) ...
+Setting up librtmp1:alpha (2.4+20151223.gitfa8646d.1-1) ...
+Setting up m4 (1.4.18-1) ...
+Setting up libicu57:alpha (57.1-8) ...
+Setting up libbsd0:alpha (0.8.6-3) ...
+Setting up libxml2:alpha (2.9.4+dfsg1-5.1) ...
+Setting up libmagic-mgc (1:5.32-1) ...
+Setting up libmagic1:alpha (1:5.32-1) ...
+Setting up libcroco3:alpha (0.6.12-1) ...
+Setting up libssh2-1:alpha (1.8.0-1) ...
+Processing triggers for libc-bin (2.25-1) ...
+Setting up autotools-dev (20161112.1+nmu1) ...
+Setting up libldap-2.4-2:alpha (2.4.45+dfsg-1) ...
+Setting up liblzma-dev:alpha (5.2.2-1.3) ...
+Setting up libkeyutils1:alpha (1.5.9-9.2) ...
+Setting up bsdmainutils (9.0.14) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libgslcblas0:alpha (2.4+dfsg-6) ...
+Setting up autopoint (0.19.8.1-4) ...
+Setting up zlib1g-dev:alpha (1:1.2.8.dfsg-5) ...
+Setting up libfile-stripnondeterminism-perl (0.040-1) ...
+Setting up libgsl23:alpha (2.4+dfsg-6) ...
+Setting up gettext (0.19.8.1-4) ...
+Setting up libgsl-dev (2.4+dfsg-6) ...
+Setting up autoconf (2.69-11) ...
+Setting up file (1:5.32-1) ...
+Setting up libkrb5support0:alpha (1.15.2-2) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up automake (1:1.15.1-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
+Setting up man-db (2.7.6.1-4) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libtool (2.4.6-2) ...
+Setting up libk5crypto3:alpha (1.15.2-2) ...
+Setting up po-debconf (1.0.20) ...
+Setting up libkrb5-3:alpha (1.15.2-2) ...
+Setting up libgssapi-krb5-2:alpha (1.15.2-2) ...
+Setting up libcurl3-gnutls:alpha (7.57.0-1) ...
+Setting up tabix (1.5-6) ...
+Setting up libhts2:alpha (1.5-6) ...
+Setting up libhts-dev:alpha (1.5-6) ...
+Setting up dh-autoreconf (15) ...
+Setting up dh-strip-nondeterminism (0.040-1) ...
+Setting up debhelper (10.10.9) ...
+Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.25-1) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+
++------------------------------------------------------------------------------+
+| Build environment |
++------------------------------------------------------------------------------+
+
+Kernel: Linux 4.13.16-titan-p1+ alpha (alpha)
+Toolchain package versions: binutils_2.29.1-11 dpkg-dev_1.19.0.4 g++-7_7.2.0-17 gcc-7_7.2.0-17 libc6.1-dev_2.25-1 libstdc++-6-dev_6.4.0-11 libstdc++-7-dev_7.2.0-17 libstdc++6_7.2.0-17 linux-libc-dev_4.14.2-1
+Package versions: adduser_3.116 apt_1.6~alpha5 aptitude_0.8.10-1 aptitude-common_0.8.10-1 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-11 binutils-alpha-linux-gnu_2.29.1-11 binutils-common_2.29.1-11 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpp_4:7.2.0-1d1 cpp-7_7.2.0-17 dash_0.5.8-2.5 debconf_1.5.65 debhelpe [...]
+
++------------------------------------------------------------------------------+
+| Build |
++------------------------------------------------------------------------------+
+
+
+Unpack source
+-------------
+
+gpgv: unknown type of key resource 'trustedkeys.kbx'
+gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
+gpgv: Signature made Mon Dec 11 14:53:09 2017 UTC
+gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
+gpgv: issuer "tillea at rki.de"
+gpgv: Can't check signature: No public key
+dpkg-source: warning: failed to verify signature on ./bcftools_1.6-1.dsc
+dpkg-source: info: extracting bcftools in /<<PKGBUILDDIR>>
+dpkg-source: info: unpacking bcftools_1.6.orig.tar.gz
+dpkg-source: info: unpacking bcftools_1.6-1.debian.tar.xz
+dpkg-source: info: applying tests-pluginpath.patch
+dpkg-source: info: applying test-regidx-unsigned-char.patch
+dpkg-source: info: applying fix-test_vcf_query.patch
+
+Check disk space
+----------------
+
+Sufficient free space for build
+
+User Environment
+----------------
+
+APT_CONFIG=/var/lib/sbuild/apt.conf
+DEB_BUILD_OPTIONS=parallel=2
+HOME=/sbuild-nonexistent
+LC_ALL=POSIX
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=experimental-alpha-sbuild
+SCHROOT_CHROOT_NAME=sid-experimental-alpha-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1001
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=sid-experimental-alpha-sbuild-f23a88de-ca28-411b-a00b-5bb9d1802077
+SCHROOT_UID=1001
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
+
+dpkg-buildpackage
+-----------------
+
+dpkg-buildpackage: info: source package bcftools
+dpkg-buildpackage: info: source version 1.6-1
+dpkg-buildpackage: info: source distribution experimental
+ dpkg-source --before-build bcftools-1.6
+dpkg-buildpackage: info: host architecture alpha
+ fakeroot debian/rules clean
+rm -f config.mk && touch config.mk
+dh clean --parallel
+ dh_auto_clean
+ make -j2 distclean
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+rm -f test/*.o test/*~
+rm -f plugins/*.so plugins/*.P
+rm -rf plugins/*.dSYM
+rm -f gmon.out *.o *~ version.h plugins/*.so plugins/*.P
+rm -rf *.dSYM plugins/*.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 '/<<PKGBUILDDIR>>'
+ dh_clean
+ debian/rules build-arch
+dh build-arch --parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_autoreconf
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+rm -f config.mk && touch config.mk
+export MAKEFLAGS="-s"; dh_autoreconf
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+dh_auto_configure -- \
+--with-htslib=system \
+--enable-gsl \
+--with-cblas=gslcblas \
+--with-bcf-plugin-dir=/usr/lib/alpha-linux-gnu/bcftools
+ ./configure --build=alpha-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/alpha-linux-gnu --libexecdir=\${prefix}/lib/alpha-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/alpha-linux-gnu/bcftools
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... no
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking shared library type... plain .so
+checking for library containing dlopen... -ldl
+checking if the compiler accepts -rdynamic... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ dh_auto_build -a -O--parallel
+ make -j2
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+echo '#define BCFTOOLS_VERSION "1.6"' > version.h
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/alpha-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c
+gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl
+gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -ldl -ldl
+gcc -rdynamic -pthread -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 vcfplugin.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 ccall.o em.o prob1.o kmin.o -l [...]
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ dh_auto_test -a -O--parallel
+ make -j2 test VERBOSE=1
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+./test/test-rbuf
+Inserted 1-9 starting at offset 5:
+ 5 6 7 8 9 0 1 2 3
+ 1 2 3 4 5 6 7 8 9
+4th is 4
+Deleting 1-2:
+ 7 8 9 0 1 2 3
+ 3 4 5 6 7 8 9
+Prepending 0-8:
+ 8 9 0 1 2 3 4 5 6 7
+ 8 7 6 5 4 3 2 1 0 3
+Expanding:
+ 8 9 10 11 12 13 14 15 16 17
+ 8 7 6 5 4 3 2 1 0 3
+./test/test-regidx
+REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix=
+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/ooDlQOhAA2/merge.a.vcf.gz 2:3199812-3199812
+.. ok
+
+test_tabix:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/ooDlQOhAA2/merge.a.bcf 2:3199812-3199812
+.. ok
+
+test_tabix:
+ tabix /tmp/ooDlQOhAA2/merge.a.vcf.gz 1:3000151-3000151
+.. ok
+
+test_tabix:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/ooDlQOhAA2/merge.a.bcf 1:3000151-3000151
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/ooDlQOhAA2/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/ooDlQOhAA2/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/ooDlQOhAA2/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/ooDlQOhAA2/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/ooDlQOhAA2/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/ooDlQOhAA2/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/ooDlQOhAA2/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/ooDlQOhAA2/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/ooDlQOhAA2/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/ooDlQOhAA2/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/ooDlQOhAA2/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/ooDlQOhAA2/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/ooDlQOhAA2/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/ooDlQOhAA2/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/ooDlQOhAA2/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/ooDlQOhAA2/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/ooDlQOhAA2/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/ooDlQOhAA2/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/ooDlQOhAA2/empty.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/ooDlQOhAA2/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/ooDlQOhAA2/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/ooDlQOhAA2/empty.bcf
+.. ok
+
+test_vcf_check:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/ooDlQOhAA2/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check_merge:
+ /<<PKGBUILDDIR>>/misc/plot-vcfstats -m /tmp/ooDlQOhAA2/check.1.chk /tmp/ooDlQOhAA2/check.2.chk /tmp/ooDlQOhAA2/check.3.chk /tmp/ooDlQOhAA2/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/ooDlQOhAA2/stats.a.vcf.gz /tmp/ooDlQOhAA2/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s B /tmp/ooDlQOhAA2/stats.a.vcf.gz /tmp/ooDlQOhAA2/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/ooDlQOhAA2/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 /tmp/ooDlQOhAA2/isec.a.vcf.gz /tmp/ooDlQOhAA2/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 /tmp/ooDlQOhAA2/isec.a.vcf.gz /tmp/ooDlQOhAA2/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/ooDlQOhAA2/isec.a.vcf.gz /tmp/ooDlQOhAA2/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/ooDlQOhAA2/isec.a.vcf.gz /tmp/ooDlQOhAA2/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -c both /tmp/ooDlQOhAA2/isec.a.vcf.gz /tmp/ooDlQOhAA2/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -c both /tmp/ooDlQOhAA2/isec.a.vcf.gz /tmp/ooDlQOhAA2/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -c any /tmp/ooDlQOhAA2/isec.a.vcf.gz /tmp/ooDlQOhAA2/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -c any /tmp/ooDlQOhAA2/isec.a.vcf.gz /tmp/ooDlQOhAA2/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -C -c any /tmp/ooDlQOhAA2/isec.a.vcf.gz /tmp/ooDlQOhAA2/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -C -c any /tmp/ooDlQOhAA2/isec.a.vcf.gz /tmp/ooDlQOhAA2/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec2:
+ /<<PKGBUILDDIR>>/bcftools isec --no-version -T /tmp/ooDlQOhAA2/isec.tab.gz /tmp/ooDlQOhAA2/isec.a.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec2:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -T /tmp/ooDlQOhAA2/isec.tab.gz /tmp/ooDlQOhAA2/isec.a.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples /tmp/ooDlQOhAA2/merge.a.vcf.gz /tmp/ooDlQOhAA2/merge.b.vcf.gz /tmp/ooDlQOhAA2/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.out
+ /<<PKGBUILDDIR>>/test/merge.abc.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples /tmp/ooDlQOhAA2/merge.a.vcf.gz /tmp/ooDlQOhAA2/merge.b.vcf.gz /tmp/ooDlQOhAA2/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.out
+ /<<PKGBUILDDIR>>/test/merge.abc.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -Fx /tmp/ooDlQOhAA2/merge.a.vcf.gz /tmp/ooDlQOhAA2/merge.b.vcf.gz /tmp/ooDlQOhAA2/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -Fx /tmp/ooDlQOhAA2/merge.a.vcf.gz /tmp/ooDlQOhAA2/merge.b.vcf.gz /tmp/ooDlQOhAA2/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -0 /tmp/ooDlQOhAA2/merge.a.vcf.gz /tmp/ooDlQOhAA2/merge.b.vcf.gz /tmp/ooDlQOhAA2/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -0 /tmp/ooDlQOhAA2/merge.a.vcf.gz /tmp/ooDlQOhAA2/merge.b.vcf.gz /tmp/ooDlQOhAA2/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m none /tmp/ooDlQOhAA2/merge.2.a.vcf.gz /tmp/ooDlQOhAA2/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.none.out
+ /<<PKGBUILDDIR>>/test/merge.2.none.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m none /tmp/ooDlQOhAA2/merge.2.a.vcf.gz /tmp/ooDlQOhAA2/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.none.out
+ /<<PKGBUILDDIR>>/test/merge.2.none.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m both /tmp/ooDlQOhAA2/merge.2.a.vcf.gz /tmp/ooDlQOhAA2/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.both.out
+ /<<PKGBUILDDIR>>/test/merge.2.both.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m both /tmp/ooDlQOhAA2/merge.2.a.vcf.gz /tmp/ooDlQOhAA2/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.both.out
+ /<<PKGBUILDDIR>>/test/merge.2.both.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m all /tmp/ooDlQOhAA2/merge.2.a.vcf.gz /tmp/ooDlQOhAA2/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.all.out
+ /<<PKGBUILDDIR>>/test/merge.2.all.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m all /tmp/ooDlQOhAA2/merge.2.a.vcf.gz /tmp/ooDlQOhAA2/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.all.out
+ /<<PKGBUILDDIR>>/test/merge.2.all.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/ooDlQOhAA2/merge.3.a.vcf.gz /tmp/ooDlQOhAA2/merge.3.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/ooDlQOhAA2/merge.3.a.vcf.gz /tmp/ooDlQOhAA2/merge.3.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m id /tmp/ooDlQOhAA2/merge.4.a.vcf.gz /tmp/ooDlQOhAA2/merge.4.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m id /tmp/ooDlQOhAA2/merge.4.a.vcf.gz /tmp/ooDlQOhAA2/merge.4.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - /tmp/ooDlQOhAA2/gvcf.merge.1.vcf.gz /tmp/ooDlQOhAA2/gvcf.merge.2.vcf.gz /tmp/ooDlQOhAA2/gvcf.merge.3.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - /tmp/ooDlQOhAA2/gvcf.merge.1.vcf.gz /tmp/ooDlQOhAA2/gvcf.merge.2.vcf.gz /tmp/ooDlQOhAA2/gvcf.merge.3.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - /tmp/ooDlQOhAA2/merge.gvcf.2.a.vcf.gz /tmp/ooDlQOhAA2/merge.gvcf.2.b.vcf.gz /tmp/ooDlQOhAA2/merge.gvcf.2.c.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - /tmp/ooDlQOhAA2/merge.gvcf.2.a.vcf.gz /tmp/ooDlQOhAA2/merge.gvcf.2.b.vcf.gz /tmp/ooDlQOhAA2/merge.gvcf.2.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - -i SRC:join /tmp/ooDlQOhAA2/merge.gvcf.3.a.vcf.gz /tmp/ooDlQOhAA2/merge.gvcf.3.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/ooDlQOhAA2/merge.gvcf.3.a.vcf.gz /tmp/ooDlQOhAA2/merge.gvcf.3.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version /tmp/ooDlQOhAA2/merge.5.a.vcf.gz /tmp/ooDlQOhAA2/merge.5.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob /tmp/ooDlQOhAA2/merge.5.a.vcf.gz /tmp/ooDlQOhAA2/merge.5.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/ooDlQOhAA2/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XRI\n' -i'XRI[*]>1111'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' /tmp/ooDlQOhAA2/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/ooDlQOhAA2/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/ooDlQOhAA2/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10' /tmp/ooDlQOhAA2/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/ooDlQOhAA2/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/ooDlQOhAA2/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/ooDlQOhAA2/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/ooDlQOhAA2/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/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/ooDlQOhAA2/view.vectors.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/query.12.out
+ /<<PKGBUILDDIR>>/test/query.12.out.new
+.. failed ...
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/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'
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/query.12.out
+ /<<PKGBUILDDIR>>/test/query.12.out.new
+.. failed ...
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' /tmp/ooDlQOhAA2/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' /tmp/ooDlQOhAA2/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' /tmp/ooDlQOhAA2/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' /tmp/ooDlQOhAA2/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/ooDlQOhAA2/query.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%LINE' /tmp/ooDlQOhAA2/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%LINE'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/ooDlQOhAA2/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/ooDlQOhAA2/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/ooDlQOhAA2/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/ooDlQOhAA2/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/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/ooDlQOhAA2/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/filter-missing-floats.vcf.gz | /<<PKGBUILDDIR>>/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:
+ /<<PKGBUILDDIR>>/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/ooDlQOhAA2/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/filter-missing-floats.vcf.gz | /<<PKGBUILDDIR>>/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:
+ /<<PKGBUILDDIR>>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/ooDlQOhAA2/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/ooDlQOhAA2/query.filter.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/query.filter.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5'
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -cx -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/ooDlQOhAA2/norm.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -cx -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/ooDlQOhAA2/norm.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- /tmp/ooDlQOhAA2/norm.split.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- /tmp/ooDlQOhAA2/norm.split.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- /tmp/ooDlQOhAA2/norm.split.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- /tmp/ooDlQOhAA2/norm.split.2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/ooDlQOhAA2/norm.split.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/ooDlQOhAA2/norm.split.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/ooDlQOhAA2/norm.merge.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/ooDlQOhAA2/norm.merge.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/ooDlQOhAA2/norm.merge.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/ooDlQOhAA2/norm.merge.2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/ooDlQOhAA2/norm.merge.3.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/ooDlQOhAA2/norm.merge.3.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.'
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ -s /tmp/ooDlQOhAA2/norm.merge.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ -s /tmp/ooDlQOhAA2/norm.merge.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -Nc s -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/ooDlQOhAA2/norm.setref.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -Nc s -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/ooDlQOhAA2/norm.setref.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/ooDlQOhAA2/norm.telomere.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/ooDlQOhAA2/norm.telomere.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/ooDlQOhAA2/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/ooDlQOhAA2/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/ooDlQOhAA2/view.vcf.gz -r20,Y
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/ooDlQOhAA2/view.vcf.gz -r20,Y | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -xs NA00003 /tmp/ooDlQOhAA2/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -xs NA00003 /tmp/ooDlQOhAA2/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/ooDlQOhAA2/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/ooDlQOhAA2/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -p /tmp/ooDlQOhAA2/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -p /tmp/ooDlQOhAA2/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -P /tmp/ooDlQOhAA2/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -P /tmp/ooDlQOhAA2/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/ooDlQOhAA2/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/ooDlQOhAA2/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -Hu /tmp/ooDlQOhAA2/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -GVsnps /tmp/ooDlQOhAA2/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -GVsnps /tmp/ooDlQOhAA2/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/ooDlQOhAA2/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/ooDlQOhAA2/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -s ^NA00003 /tmp/ooDlQOhAA2/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -s ^NA00003 /tmp/ooDlQOhAA2/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version /tmp/ooDlQOhAA2/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/view.omitgenotypes.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -G /tmp/ooDlQOhAA2/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -G /tmp/ooDlQOhAA2/view.omitgenotypes.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -HG /tmp/ooDlQOhAA2/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -a /tmp/ooDlQOhAA2/many.alleles.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -a /tmp/ooDlQOhAA2/many.alleles.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asA /tmp/ooDlQOhAA2/view.vectors.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asA /tmp/ooDlQOhAA2/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asB /tmp/ooDlQOhAA2/view.vectors.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asB /tmp/ooDlQOhAA2/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asA /tmp/ooDlQOhAA2/view.vectors.2.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asA /tmp/ooDlQOhAA2/view.vectors.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[0]="AAAAAA"' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[2]="C"' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[4]="EE"' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FRS[1]="BB"' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'TXT0="text"' /tmp/ooDlQOhAA2/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -T /<<PKGBUILDDIR>>/test/view.chrs.tab /tmp/ooDlQOhAA2/view.chrs.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -T /<<PKGBUILDDIR>>/test/view.chrs.tab /tmp/ooDlQOhAA2/view.chrs.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -i 'POS>=3062917' /tmp/ooDlQOhAA2/filter.2.vcf.gz 1:3062917-3157410
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -i 'POS>=3062917' /tmp/ooDlQOhAA2/filter.2.vcf.gz 1:3062917-3157410 | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'TXT0="text"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'TXT0="text"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FRS[1]="BB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FRS[1]="BB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[0]="AAAAAA"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[0]="AAAAAA"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[1]="BBB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[1]="BBB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[4]="EE"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[4]="EE"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/STR="XX"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/STR="XX"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -C5:nonmajor /tmp/ooDlQOhAA2/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -c6:nonmajor /tmp/ooDlQOhAA2/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -q0.3:major /tmp/ooDlQOhAA2/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/ooDlQOhAA2/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/ooDlQOhAA2/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/ooDlQOhAA2/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mg0 /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mg0 /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call_cAls:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mA -C alleles -T /tmp/ooDlQOhAA2/mpileup.tab.gz /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call_cAls:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mA -C alleles -T /tmp/ooDlQOhAA2/mpileup.tab.gz /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv /<<PKGBUILDDIR>>/test/mpileup.c.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv /<<PKGBUILDDIR>>/test/mpileup.c.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -mx -g2 -G2 /<<PKGBUILDDIR>>/test/filter.1.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -mx -g2 -G2 /<<PKGBUILDDIR>>/test/filter.1.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<<PKGBUILDDIR>>/test/filter.2.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'ALT="."' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'ALT="."' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S . -i 'FORMAT/TEST3<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S . -i 'FORMAT/TEST4<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="A"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="A"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="RR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="RR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="RA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="RA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="AR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="AR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="AA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="AA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="aA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="aA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="Aa"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="Aa"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HOM"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HOM"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HET"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HET"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HAP"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HAP"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -m 0 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.XPx31d
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -Ob -m 0 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.2U1XNl
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -m 1000 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.q9TIis
+Merging 4 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -Ob -m 1000 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.3Bc2Us
+Merging 4 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<<PKGBUILDDIR>>/test/regions.tab /tmp/ooDlQOhAA2/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<<PKGBUILDDIR>>/test/regions.tab
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /<<PKGBUILDDIR>>/test/regions.tab /tmp/ooDlQOhAA2/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ooDlQOhAA2/regions.tab.gz /tmp/ooDlQOhAA2/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ooDlQOhAA2/regions.tab.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/ooDlQOhAA2/regions.tab.gz /tmp/ooDlQOhAA2/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ooDlQOhAA2/regions.bed /tmp/ooDlQOhAA2/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ooDlQOhAA2/regions.bed
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/ooDlQOhAA2/regions.bed /tmp/ooDlQOhAA2/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ooDlQOhAA2/regions.bed.gz /tmp/ooDlQOhAA2/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ooDlQOhAA2/regions.bed.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/ooDlQOhAA2/regions.bed.gz /tmp/ooDlQOhAA2/regions.vcf.gz
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/ooDlQOhAA2/annotate.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/ooDlQOhAA2/annotate.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/ooDlQOhAA2/annotate2.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/ooDlQOhAA2/annotate2.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/ooDlQOhAA2/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/ooDlQOhAA2/annotate.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/ooDlQOhAA2/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/ooDlQOhAA2/annotate.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/ooDlQOhAA2/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/ooDlQOhAA2/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/ooDlQOhAA2/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/ooDlQOhAA2/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/ooDlQOhAA2/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/ooDlQOhAA2/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/ooDlQOhAA2/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/ooDlQOhAA2/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -x FORMAT /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -x FORMAT /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/ooDlQOhAA2/annots4.vcf.gz -c +INFO /tmp/ooDlQOhAA2/annotate4.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/ooDlQOhAA2/annots4.vcf.gz -c +INFO /tmp/ooDlQOhAA2/annotate4.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/ooDlQOhAA2/annots4.tab.gz -h /<<PKGBUILDDIR>>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<<PKGBUILDDIR>>/test/annotate4.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/ooDlQOhAA2/annots4.tab.gz -h /<<PKGBUILDDIR>>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<<PKGBUILDDIR>>/test/annotate4.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/ooDlQOhAA2/annots10.tab.gz -h /<<PKGBUILDDIR>>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<<PKGBUILDDIR>>/test/annotate10.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/ooDlQOhAA2/annots10.tab.gz -h /<<PKGBUILDDIR>>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<<PKGBUILDDIR>>/test/annotate10.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/ooDlQOhAA2/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/ooDlQOhAA2/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/ooDlQOhAA2/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/ooDlQOhAA2/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/ooDlQOhAA2/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<<PKGBUILDDIR>>/test/annotate2.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/ooDlQOhAA2/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<<PKGBUILDDIR>>/test/annotate2.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/ooDlQOhAA2/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/ooDlQOhAA2/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/ooDlQOhAA2/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/ooDlQOhAA2/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/ooDlQOhAA2/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/ooDlQOhAA2/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/ooDlQOhAA2/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/ooDlQOhAA2/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +missing2ref --no-version /tmp/ooDlQOhAA2/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +missing2ref --no-version /tmp/ooDlQOhAA2/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/ooDlQOhAA2/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/ooDlQOhAA2/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/ooDlQOhAA2/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/ooDlQOhAA2/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/ooDlQOhAA2/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<<PKGBUILDDIR>>/test/annotate9.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/ooDlQOhAA2/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<<PKGBUILDDIR>>/test/annotate9.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-AN-AC --no-version /tmp/ooDlQOhAA2/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-AN-AC --no-version /tmp/ooDlQOhAA2/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +dosage /tmp/ooDlQOhAA2/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +dosage /tmp/ooDlQOhAA2/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixploidy --no-version /tmp/ooDlQOhAA2/fixploidy.vcf.gz -- -s /<<PKGBUILDDIR>>/test/fixploidy.samples -p /<<PKGBUILDDIR>>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixploidy --no-version /tmp/ooDlQOhAA2/fixploidy.bcf -- -s /<<PKGBUILDDIR>>/test/fixploidy.samples -p /<<PKGBUILDDIR>>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/ooDlQOhAA2/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/ooDlQOhAA2/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/ooDlQOhAA2/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/ooDlQOhAA2/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/ooDlQOhAA2/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/ooDlQOhAA2/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/ooDlQOhAA2/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/ooDlQOhAA2/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/ooDlQOhAA2/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/ooDlQOhAA2/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/ooDlQOhAA2/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/ooDlQOhAA2/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/ooDlQOhAA2/view.vcf.gz -- -t AC -S /<<PKGBUILDDIR>>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/ooDlQOhAA2/view.bcf -- -t AC -S /<<PKGBUILDDIR>>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/ooDlQOhAA2/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/ooDlQOhAA2/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/ooDlQOhAA2/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/ooDlQOhAA2/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/ooDlQOhAA2/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +trio-switch-rate /tmp/ooDlQOhAA2/trio.vcf.gz -- -p /<<PKGBUILDDIR>>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +trio-switch-rate /tmp/ooDlQOhAA2/trio.bcf -- -p /<<PKGBUILDDIR>>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +ad-bias /tmp/ooDlQOhAA2/ad-bias.vcf.gz -- -s /<<PKGBUILDDIR>>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +ad-bias /tmp/ooDlQOhAA2/ad-bias.bcf -- -s /<<PKGBUILDDIR>>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +af-dist /tmp/ooDlQOhAA2/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +af-dist /tmp/ooDlQOhAA2/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixref /tmp/ooDlQOhAA2/fixref.2a.vcf.gz -- -f /<<PKGBUILDDIR>>/test/norm.fa -i /tmp/ooDlQOhAA2/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixref /tmp/ooDlQOhAA2/fixref.2a.bcf -- -f /<<PKGBUILDDIR>>/test/norm.fa -i /tmp/ooDlQOhAA2/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/ooDlQOhAA2/aa.vcf.gz -- -f /<<PKGBUILDDIR>>/test/aa.fa -c AA -h /<<PKGBUILDDIR>>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/ooDlQOhAA2/aa.bcf -- -f /<<PKGBUILDDIR>>/test/aa.fa -c AA -h /<<PKGBUILDDIR>>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/ooDlQOhAA2/ref.vcf.gz -- -f /<<PKGBUILDDIR>>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/ooDlQOhAA2/ref.bcf -- -f /<<PKGBUILDDIR>>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/ooDlQOhAA2/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/ooDlQOhAA2/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/ooDlQOhAA2/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/ooDlQOhAA2/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/ooDlQOhAA2/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/ooDlQOhAA2/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/ooDlQOhAA2/mendelian.vcf.gz -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/ooDlQOhAA2/mendelian.bcf -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/ooDlQOhAA2/mendelian.vcf.gz -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/ooDlQOhAA2/mendelian.bcf -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/ooDlQOhAA2/mendelian.vcf.gz -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/ooDlQOhAA2/mendelian.bcf -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version /tmp/ooDlQOhAA2/concat.1.a.vcf.gz /tmp/ooDlQOhAA2/concat.1.b.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob /tmp/ooDlQOhAA2/concat.1.a.vcf.gz /tmp/ooDlQOhAA2/concat.1.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version /tmp/ooDlQOhAA2/concat.1.a.bcf /tmp/ooDlQOhAA2/concat.1.b.bcf
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob /tmp/ooDlQOhAA2/concat.1.a.bcf /tmp/ooDlQOhAA2/concat.1.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -a /tmp/ooDlQOhAA2/concat.2.a.vcf.gz /tmp/ooDlQOhAA2/concat.2.b.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -a /tmp/ooDlQOhAA2/concat.2.a.vcf.gz /tmp/ooDlQOhAA2/concat.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -a /tmp/ooDlQOhAA2/concat.2.a.bcf /tmp/ooDlQOhAA2/concat.2.b.bcf
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -a /tmp/ooDlQOhAA2/concat.2.a.bcf /tmp/ooDlQOhAA2/concat.2.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -aD /tmp/ooDlQOhAA2/concat.2.a.vcf.gz /tmp/ooDlQOhAA2/concat.2.b.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -aD /tmp/ooDlQOhAA2/concat.2.a.vcf.gz /tmp/ooDlQOhAA2/concat.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -aD /tmp/ooDlQOhAA2/concat.2.a.bcf /tmp/ooDlQOhAA2/concat.2.b.bcf
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -aD /tmp/ooDlQOhAA2/concat.2.a.bcf /tmp/ooDlQOhAA2/concat.2.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -l /tmp/ooDlQOhAA2/concat.3.a.vcf.gz /tmp/ooDlQOhAA2/concat.3.b.vcf.gz /tmp/ooDlQOhAA2/concat.3.0.vcf.gz /tmp/ooDlQOhAA2/concat.3.c.vcf.gz /tmp/ooDlQOhAA2/concat.3.d.vcf.gz /tmp/ooDlQOhAA2/concat.3.e.vcf.gz /tmp/ooDlQOhAA2/concat.3.f.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -l /tmp/ooDlQOhAA2/concat.3.a.vcf.gz /tmp/ooDlQOhAA2/concat.3.b.vcf.gz /tmp/ooDlQOhAA2/concat.3.0.vcf.gz /tmp/ooDlQOhAA2/concat.3.c.vcf.gz /tmp/ooDlQOhAA2/concat.3.d.vcf.gz /tmp/ooDlQOhAA2/concat.3.e.vcf.gz /tmp/ooDlQOhAA2/concat.3.f.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -l /tmp/ooDlQOhAA2/concat.3.a.bcf /tmp/ooDlQOhAA2/concat.3.b.bcf /tmp/ooDlQOhAA2/concat.3.0.bcf /tmp/ooDlQOhAA2/concat.3.c.bcf /tmp/ooDlQOhAA2/concat.3.d.bcf /tmp/ooDlQOhAA2/concat.3.e.bcf /tmp/ooDlQOhAA2/concat.3.f.bcf
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -l /tmp/ooDlQOhAA2/concat.3.a.bcf /tmp/ooDlQOhAA2/concat.3.b.bcf /tmp/ooDlQOhAA2/concat.3.0.bcf /tmp/ooDlQOhAA2/concat.3.c.bcf /tmp/ooDlQOhAA2/concat.3.d.bcf /tmp/ooDlQOhAA2/concat.3.e.bcf /tmp/ooDlQOhAA2/concat.3.f.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Random seed for test_naive_concat: 1485111494
+.. ok
+
+test_naive_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --naive /tmp/ooDlQOhAA2/naive_concat.0.bcf /tmp/ooDlQOhAA2/naive_concat.1.bcf /tmp/ooDlQOhAA2/naive_concat.2.bcf /tmp/ooDlQOhAA2/naive_concat.3.bcf /tmp/ooDlQOhAA2/naive_concat.4.bcf /tmp/ooDlQOhAA2/naive_concat.5.bcf /tmp/ooDlQOhAA2/naive_concat.6.bcf /tmp/ooDlQOhAA2/naive_concat.7.bcf /tmp/ooDlQOhAA2/naive_concat.8.bcf /tmp/ooDlQOhAA2/naive_concat.9.bcf | /<<PKGBUILDDIR>>/bcftools view -H
+.. ok
+
+test_naive_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --naive /tmp/ooDlQOhAA2/naive_concat.0.vcf.gz /tmp/ooDlQOhAA2/naive_concat.1.vcf.gz /tmp/ooDlQOhAA2/naive_concat.2.vcf.gz /tmp/ooDlQOhAA2/naive_concat.3.vcf.gz /tmp/ooDlQOhAA2/naive_concat.4.vcf.gz /tmp/ooDlQOhAA2/naive_concat.5.vcf.gz /tmp/ooDlQOhAA2/naive_concat.6.vcf.gz /tmp/ooDlQOhAA2/naive_concat.7.vcf.gz /tmp/ooDlQOhAA2/naive_concat.8.vcf.gz /tmp/ooDlQOhAA2/naive_concat.9.vcf.gz | /<<PKGBUILDDIR>>/bcftools view -H
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /tmp/ooDlQOhAA2/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/ooDlQOhAA2/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /tmp/ooDlQOhAA2/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/ooDlQOhAA2/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /tmp/ooDlQOhAA2/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/ooDlQOhAA2/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /tmp/ooDlQOhAA2/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/ooDlQOhAA2/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /tmp/ooDlQOhAA2/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/ooDlQOhAA2/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /tmp/ooDlQOhAA2/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/ooDlQOhAA2/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /tmp/ooDlQOhAA2/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/ooDlQOhAA2/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /tmp/ooDlQOhAA2/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/ooDlQOhAA2/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /tmp/ooDlQOhAA2/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/ooDlQOhAA2/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /tmp/ooDlQOhAA2/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/ooDlQOhAA2/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /<<PKGBUILDDIR>>/test/empty.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/empty.vcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /tmp/ooDlQOhAA2/empty.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/ooDlQOhAA2/empty.bcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /tmp/ooDlQOhAA2/empty.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/ooDlQOhAA2/empty.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/ooDlQOhAA2/rename.map -Ov /tmp/ooDlQOhAA2/annotate.bcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/ooDlQOhAA2/rename.map -Ob /tmp/ooDlQOhAA2/annotate.bcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/ooDlQOhAA2/rename.map -Ov /<<PKGBUILDDIR>>/test/annotate.vcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/ooDlQOhAA2/rename.map -Ob /<<PKGBUILDDIR>>/test/annotate.vcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. /tmp/ooDlQOhAA2/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- /tmp/ooDlQOhAA2/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --tag PL /tmp/ooDlQOhAA2/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --tag PL /tmp/ooDlQOhAA2/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --vcf-ids /tmp/ooDlQOhAA2/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --vcf-ids /tmp/ooDlQOhAA2/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom /tmp/ooDlQOhAA2/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom /tmp/ooDlQOhAA2/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom --vcf-ids /tmp/ooDlQOhAA2/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom --vcf-ids /tmp/ooDlQOhAA2/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h -,.,. /tmp/ooDlQOhAA2/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h -,.,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h .,-,. /tmp/ooDlQOhAA2/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h .,-,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h .,.,- /tmp/ooDlQOhAA2/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h .,.,- 2>/dev/null
+.. ok
+
+test_vcf_convert_hls2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -H /<<PKGBUILDDIR>>/test/convert.hls.gt.hap,/<<PKGBUILDDIR>>/test/convert.hls.gt.legend,/<<PKGBUILDDIR>>/test/convert.hls.gt.samples 2>/dev/null | grep -v ^##
+.. ok
+
+test_vcf_convert_hls2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -H /<<PKGBUILDDIR>>/test/convert.hls.gt.hap,/<<PKGBUILDDIR>>/test/convert.hls.gt.legend,/<<PKGBUILDDIR>>/test/convert.hls.gt.samples -Ou 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##
+.. ok
+
+test_vcf_convert_hs2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample2vcf /<<PKGBUILDDIR>>/test/convert.hs.gt.hap,/<<PKGBUILDDIR>>/test/convert.hs.gt.samples 2>/dev/null | grep -v ^##
+.. ok
+
+test_vcf_convert_hs2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample2vcf /<<PKGBUILDDIR>>/test/convert.hs.gt.hap,/<<PKGBUILDDIR>>/test/convert.hs.gt.samples -Ou 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample -,. /tmp/ooDlQOhAA2/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --hapsample -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample .,- /tmp/ooDlQOhAA2/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --hapsample .,- 2>/dev/null
+.. ok
+
+test_vcf_convert_gvcf:
+ /<<PKGBUILDDIR>>/bcftools convert --no-version --gvcf2vcf -f /<<PKGBUILDDIR>>/test/gvcf.fa /tmp/ooDlQOhAA2/convert.gvcf.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert_gvcf:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/ooDlQOhAA2/convert.gvcf.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --gvcf2vcf -f /<<PKGBUILDDIR>>/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools
+.. ok
+
+test_vcf_convert_tsv2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /<<PKGBUILDDIR>>/test/23andme.fa --tsv2vcf /<<PKGBUILDDIR>>/test/convert.23andme 2>/dev/null
+.. ok
+
+test_vcf_convert_tsv2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /<<PKGBUILDDIR>>/test/23andme.fa --tsv2vcf /<<PKGBUILDDIR>>/test/convert.23andme 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/ooDlQOhAA2/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/ooDlQOhAA2/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/ooDlQOhAA2/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/ooDlQOhAA2/consensus.1.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/ooDlQOhAA2/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/ooDlQOhAA2/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/ooDlQOhAA2/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/ooDlQOhAA2/consensus.2.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/ooDlQOhAA2/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -I -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/ooDlQOhAA2/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -I -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/ooDlQOhAA2/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/ooDlQOhAA2/consensus.3.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/ooDlQOhAA2/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/ooDlQOhAA2/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -c /tmp/ooDlQOhAA2/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/ooDlQOhAA2/consensus.4.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/ooDlQOhAA2/consensus2.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus2.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/ooDlQOhAA2/consensus2.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus2.fa -H 2 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/ooDlQOhAA2/empty.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa 2>/dev/null
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -b /tmp/ooDlQOhAA2/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/ooDlQOhAA2/mpileup.bam.urllist 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -b /tmp/ooDlQOhAA2/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/ooDlQOhAA2/mpileup.cram.urllist 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_csq:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq.fa -g /<<PKGBUILDDIR>>/test/csq.gff3 /<<PKGBUILDDIR>>/test/csq.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq.gff3 ...
+Indexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.gff /<<PKGBUILDDIR>>/test/csq/ENST00000545279/splice-region-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.gff ...
+Indexed 1 transcripts, 9 exons, 7 CDSs, 4 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.gff /<<PKGBUILDDIR>>/test/csq/ENST00000390520/deletion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.gff /<<PKGBUILDDIR>>/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff /<<PKGBUILDDIR>>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff /<<PKGBUILDDIR>>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff /<<PKGBUILDDIR>>/test/csq/ENST00000218032/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff /<<PKGBUILDDIR>>/test/csq/ENST00000218032/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff /<<PKGBUILDDIR>>/test/csq/ENST00000373833/boundary-insertion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff /<<PKGBUILDDIR>>/test/csq/ENST00000373833/boundary-insertion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.gff /<<PKGBUILDDIR>>/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.gff /<<PKGBUILDDIR>>/test/csq/ENST00000413103/long-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.gff ...
+Indexed 1 transcripts, 2 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.gff /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.gff /<<PKGBUILDDIR>>/test/csq/ENST00000557788/long-overlap-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.gff /<<PKGBUILDDIR>>/test/csq/ENST00000519442/synon-splice-region-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.gff /<<PKGBUILDDIR>>/test/csq/ENST00000436063/insert-before-utr.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.gff ...
+Indexed 1 transcripts, 7 exons, 7 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff /<<PKGBUILDDIR>>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff /<<PKGBUILDDIR>>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff /<<PKGBUILDDIR>>/test/csq/ENST00000303039/not-a-stop.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff /<<PKGBUILDDIR>>/test/csq/ENST00000303039/not-a-stop.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.gff /<<PKGBUILDDIR>>/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.gff ...
+Indexed 1 transcripts, 26 exons, 26 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.gff /<<PKGBUILDDIR>>/test/csq/ENST00000593942/last-codon-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.gff ...
+Indexed 1 transcripts, 7 exons, 4 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.gff /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.gff ...
+Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520868/long-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.gff /<<PKGBUILDDIR>>/test/csq/ENST00000409523/long-overlapping-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff /<<PKGBUILDDIR>>/test/csq/ENST00000329454/boundary-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff /<<PKGBUILDDIR>>/test/csq/ENST00000329454/boundary-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.gff /<<PKGBUILDDIR>>/test/csq/ENST00000357367/stop-retained.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.gff ...
+Indexed 1 transcripts, 4 exons, 3 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff /<<PKGBUILDDIR>>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff /<<PKGBUILDDIR>>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff /<<PKGBUILDDIR>>/test/csq/ENST00000542803/splice-region.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff /<<PKGBUILDDIR>>/test/csq/ENST00000542803/splice-region.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.gff /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.gff /<<PKGBUILDDIR>>/test/csq/ENST00000381157/haploid-diploid.vcf | /<<PKGBUILDDIR>>/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 0 UTRs
+Calling...
+Warning: Skipping site with non-diploid/non-haploid genotypes at X:31180 C>T
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff /<<PKGBUILDDIR>>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff /<<PKGBUILDDIR>>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff /<<PKGBUILDDIR>>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff /<<PKGBUILDDIR>>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.gff /<<PKGBUILDDIR>>/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.fa -g /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.gff /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/synon.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.gff ...
+Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff /<<PKGBUILDDIR>>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff /<<PKGBUILDDIR>>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff /<<PKGBUILDDIR>>/test/csq/ENST00000318249/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff /<<PKGBUILDDIR>>/test/csq/ENST00000318249/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520795/long-inside-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520795/long-inside-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ambiguous.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/snps.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/snps.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/insert3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/insert3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.gff /<<PKGBUILDDIR>>/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.gff ...
+Indexed 1 transcripts, 7 exons, 6 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.gff /<<PKGBUILDDIR>>/test/csq/ENST00000256452/intron.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.gff ...
+Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.gff /<<PKGBUILDDIR>>/test/csq/ENST00000420670/start-stop-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.gff ...
+Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs
+Calling...
+.. ok
+
+
+Number of tests:
+ total .. 728
+ passed .. 714
+ failed .. 14
+
+Makefile:246: recipe for target 'test-plugins' failed
+make[1]: *** [test-plugins] Error 1
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+dh_auto_test: make -j2 test VERBOSE=1 returned exit code 2
+debian/rules:7: recipe for target 'build-arch' failed
+make: *** [build-arch] Error 2
+dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
+--------------------------------------------------------------------------------
+Build finished at 2017-12-12T03:07:10Z
+
+Finished
+--------
+
+
++------------------------------------------------------------------------------+
+| Cleanup |
++------------------------------------------------------------------------------+
+
+Purging /<<BUILDDIR>>
+Not cleaning session: cloned chroot in use
+E: Build failure (dpkg-buildpackage died)
+
++------------------------------------------------------------------------------+
+| Summary |
++------------------------------------------------------------------------------+
+
+Build Architecture: alpha
+Build Type: any
+Build-Space: 25572
+Build-Time: 224
+Distribution: experimental
+Fail-Stage: build
+Host Architecture: alpha
+Install-Time: 73
+Job: bcftools_1.6-1
+Machine Architecture: alpha
+Package: bcftools
+Package-Time: 337
+Source-Version: 1.6-1
+Space: 25572
+Status: attempted
+Version: 1.6-1
+--------------------------------------------------------------------------------
+Finished at 2017-12-12T03:07:10Z
+Build needed 00:05:37, 25572k disk space
diff --git a/bcftools_1.6-1_i386.log b/bcftools_1.6-1_i386.log
new file mode 100644
index 0000000..0f06a64
--- /dev/null
+++ b/bcftools_1.6-1_i386.log
@@ -0,0 +1,4289 @@
+
+sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on x86-csail-01.debian.org
+
++==============================================================================+
+| bcftools 1.6-1 (i386) Mon, 11 Dec 2017 16:14:14 +0000 |
++==============================================================================+
+
+Package: bcftools
+Version: 1.6-1
+Source Version: 1.6-1
+Distribution: experimental
+Machine Architecture: amd64
+Host Architecture: i386
+Build Architecture: i386
+Build Type: any
+
+I: NOTICE: Log filtering will replace 'var/run/schroot/mount/experimental-i386-sbuild-6fc96d61-f17a-4ba5-a536-28f5e399237d' with '<<CHROOT>>'
+
++------------------------------------------------------------------------------+
+| Update chroot |
++------------------------------------------------------------------------------+
+
+Get:1 http://debian.csail.mit.edu/debian unstable InRelease [240 kB]
+Get:2 http://debian.csail.mit.edu/debian experimental InRelease [107 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:4 http://incoming.debian.org/debian-buildd buildd-experimental InRelease [58.9 kB]
+Get:5 http://debian.csail.mit.edu/debian unstable/non-free Sources [83.9 kB]
+Get:6 http://debian.csail.mit.edu/debian unstable/main Sources [7953 kB]
+Get:7 http://debian.csail.mit.edu/debian unstable/contrib Sources [50.5 kB]
+Get:8 http://debian.csail.mit.edu/debian unstable/contrib i386 Packages [55.2 kB]
+Get:9 http://debian.csail.mit.edu/debian unstable/main i386 Packages [7791 kB]
+Get:10 http://ftp.debian.org/debian unstable InRelease [240 kB]
+Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [123 kB]
+Get:12 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1916 B]
+Get:13 http://incoming.debian.org/debian-buildd buildd-unstable/main i386 Packages [139 kB]
+Get:14 http://incoming.debian.org/debian-buildd buildd-unstable/contrib i386 Packages [1700 B]
+Get:15 http://debian.csail.mit.edu/debian experimental/contrib Sources [1692 B]
+Get:16 http://debian.csail.mit.edu/debian experimental/non-free Sources [3012 B]
+Get:17 http://debian.csail.mit.edu/debian experimental/main Sources [262 kB]
+Get:18 http://debian.csail.mit.edu/debian experimental/main i386 Packages [446 kB]
+Get:19 http://incoming.debian.org/debian-buildd buildd-experimental/main Sources [30.7 kB]
+Get:20 http://incoming.debian.org/debian-buildd buildd-experimental/main i386 Packages [56.7 kB]
+Get:21 http://debian.csail.mit.edu/debian experimental/contrib i386 Packages [2324 B]
+Get:22 http://incoming.debian.org/debian-buildd buildd-experimental/contrib i386 Packages [768 B]
+Get:23 http://ftp.debian.org/debian experimental InRelease [107 kB]
+Get:24 http://ftp.debian.org/debian unstable/contrib Sources [50.5 kB]
+Get:25 http://ftp.debian.org/debian unstable/main Sources [7953 kB]
+Get:26 http://ftp.debian.org/debian unstable/non-free Sources [83.9 kB]
+Get:27 http://ftp.debian.org/debian unstable/contrib i386 Packages [55.2 kB]
+Get:28 http://ftp.debian.org/debian unstable/main i386 Packages [7791 kB]
+Get:29 http://ftp.debian.org/debian experimental/main Sources [262 kB]
+Get:30 http://ftp.debian.org/debian experimental/non-free Sources [3012 B]
+Get:31 http://ftp.debian.org/debian experimental/contrib Sources [1692 B]
+Get:32 http://ftp.debian.org/debian experimental/contrib i386 Packages [2324 B]
+Get:33 http://ftp.debian.org/debian experimental/main i386 Packages [446 kB]
+Fetched 34.5 MB in 7s (4343 kB/s)
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Fetch source files |
++------------------------------------------------------------------------------+
+
+
+Check APT
+---------
+
+Checking available source versions...
+
+Download source files with APT
+------------------------------
+
+Reading package lists...
+NOTICE: 'bcftools' packaging is maintained in the 'Git' version control system at:
+https://anonscm.debian.org/git/debian-med/bcftools.git
+Please use:
+git clone https://anonscm.debian.org/git/debian-med/bcftools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 2342 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (dsc) [2110 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (tar) [2333 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (diff) [6088 B]
+Fetched 2342 kB in 0s (33.6 MB/s)
+Download complete and in download only mode
+I: NOTICE: Log filtering will replace 'build/bcftools-KsMvJL/bcftools-1.6' with '<<PKGBUILDDIR>>'
+I: NOTICE: Log filtering will replace 'build/bcftools-KsMvJL' with '<<BUILDDIR>>'
+
++------------------------------------------------------------------------------+
+| 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 '/<<BUILDDIR>>/resolver-AFLnae/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:/<<BUILDDIR>>/resolver-AFLnae/apt_archive ./ InRelease
+Get:2 copy:/<<BUILDDIR>>/resolver-AFLnae/apt_archive ./ Release [957 B]
+Ign:3 copy:/<<BUILDDIR>>/resolver-AFLnae/apt_archive ./ Release.gpg
+Get:4 copy:/<<BUILDDIR>>/resolver-AFLnae/apt_archive ./ Sources [349 B]
+Get:5 copy:/<<BUILDDIR>>/resolver-AFLnae/apt_archive ./ Packages [432 B]
+Fetched 1738 B in 0s (93.5 kB/s)
+Reading package lists...
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Install core build dependencies (aptitude-based resolver) |
++------------------------------------------------------------------------------+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following additional packages will be installed:
+ aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+Suggested packages:
+ aptitude-doc-en | aptitude-doc apt-xapian-index debtags tasksel
+ libcwidget-dev xapian-tools
+Recommended packages:
+ libparse-debianchangelog-perl
+The following NEW packages will be installed:
+ aptitude aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+0 upgraded, 9 newly installed, 0 to remove and 1 not upgraded.
+Need to get 5636 kB of archives.
+After this operation, 22.2 MB of additional disk space will be used.
+Get:1 http://debian.csail.mit.edu/debian unstable/main i386 libxapian30 i386 1.4.5-1 [1315 kB]
+Get:2 http://debian.csail.mit.edu/debian unstable/main i386 libsqlite3-0 i386 3.21.0-1 [623 kB]
+Get:3 http://debian.csail.mit.edu/debian unstable/main i386 aptitude-common all 0.8.10-1 [1591 kB]
+Get:4 http://debian.csail.mit.edu/debian unstable/main i386 libboost-system1.62.0 i386 1.62.0+dfsg-4+b2 [33.0 kB]
+Get:5 http://debian.csail.mit.edu/debian unstable/main i386 libboost-filesystem1.62.0 i386 1.62.0+dfsg-4+b2 [67.9 kB]
+Get:6 http://debian.csail.mit.edu/debian unstable/main i386 libboost-iostreams1.62.0 i386 1.62.0+dfsg-4+b2 [53.2 kB]
+Get:7 http://debian.csail.mit.edu/debian unstable/main i386 libsigc++-2.0-0v5 i386 2.10.0-1 [62.1 kB]
+Get:8 http://debian.csail.mit.edu/debian unstable/main i386 libcwidget3v5 i386 0.5.17-6 [330 kB]
+Get:9 http://debian.csail.mit.edu/debian unstable/main i386 aptitude i386 0.8.10-1 [1561 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 5636 kB in 0s (20.3 MB/s)
+Selecting previously unselected package libxapian30:i386.
+(Reading database ... 11727 files and directories currently installed.)
+Preparing to unpack .../0-libxapian30_1.4.5-1_i386.deb ...
+Unpacking libxapian30:i386 (1.4.5-1) ...
+Selecting previously unselected package libsqlite3-0:i386.
+Preparing to unpack .../1-libsqlite3-0_3.21.0-1_i386.deb ...
+Unpacking libsqlite3-0:i386 (3.21.0-1) ...
+Selecting previously unselected package aptitude-common.
+Preparing to unpack .../2-aptitude-common_0.8.10-1_all.deb ...
+Unpacking aptitude-common (0.8.10-1) ...
+Selecting previously unselected package libboost-system1.62.0:i386.
+Preparing to unpack .../3-libboost-system1.62.0_1.62.0+dfsg-4+b2_i386.deb ...
+Unpacking libboost-system1.62.0:i386 (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libboost-filesystem1.62.0:i386.
+Preparing to unpack .../4-libboost-filesystem1.62.0_1.62.0+dfsg-4+b2_i386.deb ...
+Unpacking libboost-filesystem1.62.0:i386 (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libboost-iostreams1.62.0:i386.
+Preparing to unpack .../5-libboost-iostreams1.62.0_1.62.0+dfsg-4+b2_i386.deb ...
+Unpacking libboost-iostreams1.62.0:i386 (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libsigc++-2.0-0v5:i386.
+Preparing to unpack .../6-libsigc++-2.0-0v5_2.10.0-1_i386.deb ...
+Unpacking libsigc++-2.0-0v5:i386 (2.10.0-1) ...
+Selecting previously unselected package libcwidget3v5:i386.
+Preparing to unpack .../7-libcwidget3v5_0.5.17-6_i386.deb ...
+Unpacking libcwidget3v5:i386 (0.5.17-6) ...
+Selecting previously unselected package aptitude.
+Preparing to unpack .../8-aptitude_0.8.10-1_i386.deb ...
+Unpacking aptitude (0.8.10-1) ...
+Setting up libxapian30:i386 (1.4.5-1) ...
+Setting up aptitude-common (0.8.10-1) ...
+Setting up libboost-iostreams1.62.0:i386 (1.62.0+dfsg-4+b2) ...
+Processing triggers for libc-bin (2.25-3) ...
+Setting up libsqlite3-0:i386 (3.21.0-1) ...
+Setting up libsigc++-2.0-0v5:i386 (2.10.0-1) ...
+Setting up libboost-system1.62.0:i386 (1.62.0+dfsg-4+b2) ...
+Setting up libboost-filesystem1.62.0:i386 (1.62.0+dfsg-4+b2) ...
+Setting up libcwidget3v5:i386 (0.5.17-6) ...
+Setting up aptitude (0.8.10-1) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode
+Processing triggers for libc-bin (2.25-3) ...
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-core-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-core-dummy:i386
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+0 packages upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
+Need to get 852 B of archives. After unpacking 0 B will be used.
+Writing extended state information...
+Get: 1 copy:/<<BUILDDIR>>/resolver-AFLnae/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
+Fetched 852 B in 0s (0 B/s)
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11984 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_i386.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+
++------------------------------------------------------------------------------+
+| Check architectures |
++------------------------------------------------------------------------------+
+
+Arch check ok (i386 included in any)
+
++------------------------------------------------------------------------------+
+| Install package build dependencies |
++------------------------------------------------------------------------------+
+
+
+Setup apt archive
+-----------------
+
+Merged Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+Filtered Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<<BUILDDIR>>/resolver-AFLnae/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:/<<BUILDDIR>>/resolver-AFLnae/apt_archive ./ InRelease
+Get:2 copy:/<<BUILDDIR>>/resolver-AFLnae/apt_archive ./ Release [963 B]
+Ign:3 copy:/<<BUILDDIR>>/resolver-AFLnae/apt_archive ./ Release.gpg
+Get:4 copy:/<<BUILDDIR>>/resolver-AFLnae/apt_archive ./ Sources [546 B]
+Get:5 copy:/<<BUILDDIR>>/resolver-AFLnae/apt_archive ./ Packages [616 B]
+Fetched 2125 B in 0s (108 kB/s)
+Reading package lists...
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Install bcftools build dependencies (aptitude-based resolver) |
++------------------------------------------------------------------------------+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+aptitude is already the newest version (0.8.10-1).
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-bcftools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-bcftool [...]
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libbz2-dev{a} libcroco3{a} libcurl3-gnutls{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu57{a} libio-pty-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} l [...]
+The following packages are RECOMMENDED but will NOT be installed:
+ bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules publicsuffix shared-mime-info wget xdg-user-dirs
+0 packages upgraded, 56 newly installed, 0 to remove and 1 not upgraded.
+Need to get 26.8 MB of archives. After unpacking 89.2 MB will be used.
+Writing extended state information...
+Get: 1 copy:/<<BUILDDIR>>/resolver-AFLnae/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [908 B]
+Get: 2 http://debian.csail.mit.edu/debian unstable/main i386 groff-base i386 1.22.3-9 [1186 kB]
+Get: 3 http://debian.csail.mit.edu/debian unstable/main i386 libbsd0 i386 0.8.6-3 [94.6 kB]
+Get: 4 http://debian.csail.mit.edu/debian unstable/main i386 libncurses5 i386 6.0+20171125-1 [102 kB]
+Get: 5 http://debian.csail.mit.edu/debian unstable/main i386 bsdmainutils i386 9.0.14 [189 kB]
+Get: 6 http://debian.csail.mit.edu/debian unstable/main i386 libpipeline1 i386 1.5.0-1 [31.0 kB]
+Get: 7 http://debian.csail.mit.edu/debian unstable/main i386 man-db i386 2.7.6.1-4 [1056 kB]
+Get: 8 http://debian.csail.mit.edu/debian unstable/main i386 libssl1.1 i386 1.1.0g-2 [1342 kB]
+Get: 9 http://debian.csail.mit.edu/debian unstable/main i386 libmagic-mgc i386 1:5.32-1 [225 kB]
+Get: 10 http://debian.csail.mit.edu/debian unstable/main i386 libmagic1 i386 1:5.32-1 [118 kB]
+Get: 11 http://debian.csail.mit.edu/debian unstable/main i386 file i386 1:5.32-1 [64.3 kB]
+Get: 12 http://debian.csail.mit.edu/debian unstable/main i386 gettext-base i386 0.19.8.1-4 [123 kB]
+Get: 13 http://debian.csail.mit.edu/debian unstable/main i386 libkeyutils1 i386 1.5.9-9.2 [13.1 kB]
+Get: 14 http://debian.csail.mit.edu/debian unstable/main i386 libkrb5support0 i386 1.15.2-2 [64.4 kB]
+Get: 15 http://debian.csail.mit.edu/debian unstable/main i386 libk5crypto3 i386 1.15.2-2 [125 kB]
+Get: 16 http://debian.csail.mit.edu/debian unstable/main i386 libkrb5-3 i386 1.15.2-2 [338 kB]
+Get: 17 http://debian.csail.mit.edu/debian unstable/main i386 libgssapi-krb5-2 i386 1.15.2-2 [166 kB]
+Get: 18 http://debian.csail.mit.edu/debian unstable/main i386 libsasl2-modules-db i386 2.1.27~101-g0780600+dfsg-3 [69.2 kB]
+Get: 19 http://debian.csail.mit.edu/debian unstable/main i386 libsasl2-2 i386 2.1.27~101-g0780600+dfsg-3 [108 kB]
+Get: 20 http://debian.csail.mit.edu/debian unstable/main i386 libldap-common all 2.4.45+dfsg-1 [87.0 kB]
+Get: 21 http://debian.csail.mit.edu/debian unstable/main i386 libldap-2.4-2 i386 2.4.45+dfsg-1 [234 kB]
+Get: 22 http://debian.csail.mit.edu/debian unstable/main i386 libicu57 i386 57.1-8 [7840 kB]
+Get: 23 http://debian.csail.mit.edu/debian unstable/main i386 libxml2 i386 2.9.4+dfsg1-5.1 [764 kB]
+Get: 24 http://debian.csail.mit.edu/debian unstable/main i386 libsigsegv2 i386 2.11-1 [30.1 kB]
+Get: 25 http://debian.csail.mit.edu/debian unstable/main i386 m4 i386 1.4.18-1 [205 kB]
+Get: 26 http://debian.csail.mit.edu/debian unstable/main i386 autoconf all 2.69-11 [341 kB]
+Get: 27 http://debian.csail.mit.edu/debian unstable/main i386 autotools-dev all 20161112.1+nmu1 [74.2 kB]
+Get: 28 http://debian.csail.mit.edu/debian unstable/main i386 automake all 1:1.15.1-3 [736 kB]
+Get: 29 http://debian.csail.mit.edu/debian unstable/main i386 autopoint all 0.19.8.1-4 [434 kB]
+Get: 30 http://debian.csail.mit.edu/debian unstable/main i386 libtool all 2.4.6-2 [545 kB]
+Get: 31 http://debian.csail.mit.edu/debian unstable/main i386 dh-autoreconf all 15 [16.2 kB]
+Get: 32 http://debian.csail.mit.edu/debian unstable/main i386 libarchive-zip-perl all 1.59-1 [95.5 kB]
+Get: 33 http://debian.csail.mit.edu/debian unstable/main i386 libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
+Get: 34 http://debian.csail.mit.edu/debian unstable/main i386 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get: 35 http://debian.csail.mit.edu/debian unstable/main i386 dh-strip-nondeterminism all 0.040-1 [11.8 kB]
+Get: 36 http://debian.csail.mit.edu/debian unstable/main i386 libglib2.0-0 i386 2.54.2-1 [2888 kB]
+Get: 37 http://debian.csail.mit.edu/debian unstable/main i386 libcroco3 i386 0.6.12-1 [150 kB]
+Get: 38 http://debian.csail.mit.edu/debian unstable/main i386 gettext i386 0.19.8.1-4 [1311 kB]
+Get: 39 http://debian.csail.mit.edu/debian unstable/main i386 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get: 40 http://debian.csail.mit.edu/debian unstable/main i386 po-debconf all 1.0.20 [247 kB]
+Get: 41 http://debian.csail.mit.edu/debian unstable/main i386 debhelper all 10.10.9 [975 kB]
+Get: 42 http://debian.csail.mit.edu/debian unstable/main i386 libbz2-dev i386 1.0.6-8.1 [30.0 kB]
+Get: 43 http://debian.csail.mit.edu/debian unstable/main i386 libnghttp2-14 i386 1.28.0-1 [88.9 kB]
+Get: 44 http://debian.csail.mit.edu/debian unstable/main i386 libpsl5 i386 0.19.1-4 [45.1 kB]
+Get: 45 http://debian.csail.mit.edu/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-1+b1 [64.4 kB]
+Get: 46 http://debian.csail.mit.edu/debian unstable/main i386 libssh2-1 i386 1.8.0-1 [145 kB]
+Get: 47 http://debian.csail.mit.edu/debian unstable/main i386 libcurl3-gnutls i386 7.57.0-1 [333 kB]
+Get: 48 http://debian.csail.mit.edu/debian unstable/main i386 libgslcblas0 i386 2.4+dfsg-6 [97.4 kB]
+Get: 49 http://debian.csail.mit.edu/debian unstable/main i386 libgsl23 i386 2.4+dfsg-6 [828 kB]
+Get: 50 http://debian.csail.mit.edu/debian unstable/main i386 libgsl-dev i386 2.4+dfsg-6 [1042 kB]
+Get: 51 http://debian.csail.mit.edu/debian unstable/main i386 libhts2 i386 1.5-6 [317 kB]
+Get: 52 http://debian.csail.mit.edu/debian unstable/main i386 liblzma-dev i386 5.2.2-1.3 [302 kB]
+Get: 53 http://debian.csail.mit.edu/debian unstable/main i386 tabix i386 1.5-6 [341 kB]
+Get: 54 http://debian.csail.mit.edu/debian unstable/main i386 libhts-dev i386 1.5-6 [397 kB]
+Get: 55 http://debian.csail.mit.edu/debian unstable/main i386 libio-pty-perl i386 1:1.08-1.1+b4 [34.3 kB]
+Get: 56 http://debian.csail.mit.edu/debian unstable/main i386 zlib1g-dev i386 1:1.2.8.dfsg-5 [207 kB]
+Fetched 26.8 MB in 1s (15.9 MB/s)
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package groff-base.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11984 files and directories currently installed.)
+Preparing to unpack .../00-groff-base_1.22.3-9_i386.deb ...
+Unpacking groff-base (1.22.3-9) ...
+Selecting previously unselected package libbsd0:i386.
+Preparing to unpack .../01-libbsd0_0.8.6-3_i386.deb ...
+Unpacking libbsd0:i386 (0.8.6-3) ...
+Selecting previously unselected package libncurses5:i386.
+Preparing to unpack .../02-libncurses5_6.0+20171125-1_i386.deb ...
+Unpacking libncurses5:i386 (6.0+20171125-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../03-bsdmainutils_9.0.14_i386.deb ...
+Unpacking bsdmainutils (9.0.14) ...
+Selecting previously unselected package libpipeline1:i386.
+Preparing to unpack .../04-libpipeline1_1.5.0-1_i386.deb ...
+Unpacking libpipeline1:i386 (1.5.0-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../05-man-db_2.7.6.1-4_i386.deb ...
+Unpacking man-db (2.7.6.1-4) ...
+Selecting previously unselected package libssl1.1:i386.
+Preparing to unpack .../06-libssl1.1_1.1.0g-2_i386.deb ...
+Unpacking libssl1.1:i386 (1.1.0g-2) ...
+Selecting previously unselected package libmagic-mgc.
+Preparing to unpack .../07-libmagic-mgc_1%3a5.32-1_i386.deb ...
+Unpacking libmagic-mgc (1:5.32-1) ...
+Selecting previously unselected package libmagic1:i386.
+Preparing to unpack .../08-libmagic1_1%3a5.32-1_i386.deb ...
+Unpacking libmagic1:i386 (1:5.32-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../09-file_1%3a5.32-1_i386.deb ...
+Unpacking file (1:5.32-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../10-gettext-base_0.19.8.1-4_i386.deb ...
+Unpacking gettext-base (0.19.8.1-4) ...
+Selecting previously unselected package libkeyutils1:i386.
+Preparing to unpack .../11-libkeyutils1_1.5.9-9.2_i386.deb ...
+Unpacking libkeyutils1:i386 (1.5.9-9.2) ...
+Selecting previously unselected package libkrb5support0:i386.
+Preparing to unpack .../12-libkrb5support0_1.15.2-2_i386.deb ...
+Unpacking libkrb5support0:i386 (1.15.2-2) ...
+Selecting previously unselected package libk5crypto3:i386.
+Preparing to unpack .../13-libk5crypto3_1.15.2-2_i386.deb ...
+Unpacking libk5crypto3:i386 (1.15.2-2) ...
+Selecting previously unselected package libkrb5-3:i386.
+Preparing to unpack .../14-libkrb5-3_1.15.2-2_i386.deb ...
+Unpacking libkrb5-3:i386 (1.15.2-2) ...
+Selecting previously unselected package libgssapi-krb5-2:i386.
+Preparing to unpack .../15-libgssapi-krb5-2_1.15.2-2_i386.deb ...
+Unpacking libgssapi-krb5-2:i386 (1.15.2-2) ...
+Selecting previously unselected package libsasl2-modules-db:i386.
+Preparing to unpack .../16-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3_i386.deb ...
+Unpacking libsasl2-modules-db:i386 (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libsasl2-2:i386.
+Preparing to unpack .../17-libsasl2-2_2.1.27~101-g0780600+dfsg-3_i386.deb ...
+Unpacking libsasl2-2:i386 (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libldap-common.
+Preparing to unpack .../18-libldap-common_2.4.45+dfsg-1_all.deb ...
+Unpacking libldap-common (2.4.45+dfsg-1) ...
+Selecting previously unselected package libldap-2.4-2:i386.
+Preparing to unpack .../19-libldap-2.4-2_2.4.45+dfsg-1_i386.deb ...
+Unpacking libldap-2.4-2:i386 (2.4.45+dfsg-1) ...
+Selecting previously unselected package libicu57:i386.
+Preparing to unpack .../20-libicu57_57.1-8_i386.deb ...
+Unpacking libicu57:i386 (57.1-8) ...
+Selecting previously unselected package libxml2:i386.
+Preparing to unpack .../21-libxml2_2.9.4+dfsg1-5.1_i386.deb ...
+Unpacking libxml2:i386 (2.9.4+dfsg1-5.1) ...
+Selecting previously unselected package libsigsegv2:i386.
+Preparing to unpack .../22-libsigsegv2_2.11-1_i386.deb ...
+Unpacking libsigsegv2:i386 (2.11-1) ...
+Selecting previously unselected package m4.
+Preparing to unpack .../23-m4_1.4.18-1_i386.deb ...
+Unpacking m4 (1.4.18-1) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../24-autoconf_2.69-11_all.deb ...
+Unpacking autoconf (2.69-11) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../25-autotools-dev_20161112.1+nmu1_all.deb ...
+Unpacking autotools-dev (20161112.1+nmu1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../26-automake_1%3a1.15.1-3_all.deb ...
+Unpacking automake (1:1.15.1-3) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../27-autopoint_0.19.8.1-4_all.deb ...
+Unpacking autopoint (0.19.8.1-4) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../28-libtool_2.4.6-2_all.deb ...
+Unpacking libtool (2.4.6-2) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../29-dh-autoreconf_15_all.deb ...
+Unpacking dh-autoreconf (15) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../30-libarchive-zip-perl_1.59-1_all.deb ...
+Unpacking libarchive-zip-perl (1.59-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../31-libfile-stripnondeterminism-perl_0.040-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.040-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../32-libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../33-dh-strip-nondeterminism_0.040-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.040-1) ...
+Selecting previously unselected package libglib2.0-0:i386.
+Preparing to unpack .../34-libglib2.0-0_2.54.2-1_i386.deb ...
+Unpacking libglib2.0-0:i386 (2.54.2-1) ...
+Selecting previously unselected package libcroco3:i386.
+Preparing to unpack .../35-libcroco3_0.6.12-1_i386.deb ...
+Unpacking libcroco3:i386 (0.6.12-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../36-gettext_0.19.8.1-4_i386.deb ...
+Unpacking gettext (0.19.8.1-4) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../37-intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../38-po-debconf_1.0.20_all.deb ...
+Unpacking po-debconf (1.0.20) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../39-debhelper_10.10.9_all.deb ...
+Unpacking debhelper (10.10.9) ...
+Selecting previously unselected package libbz2-dev:i386.
+Preparing to unpack .../40-libbz2-dev_1.0.6-8.1_i386.deb ...
+Unpacking libbz2-dev:i386 (1.0.6-8.1) ...
+Selecting previously unselected package libnghttp2-14:i386.
+Preparing to unpack .../41-libnghttp2-14_1.28.0-1_i386.deb ...
+Unpacking libnghttp2-14:i386 (1.28.0-1) ...
+Selecting previously unselected package libpsl5:i386.
+Preparing to unpack .../42-libpsl5_0.19.1-4_i386.deb ...
+Unpacking libpsl5:i386 (0.19.1-4) ...
+Selecting previously unselected package librtmp1:i386.
+Preparing to unpack .../43-librtmp1_2.4+20151223.gitfa8646d.1-1+b1_i386.deb ...
+Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-1+b1) ...
+Selecting previously unselected package libssh2-1:i386.
+Preparing to unpack .../44-libssh2-1_1.8.0-1_i386.deb ...
+Unpacking libssh2-1:i386 (1.8.0-1) ...
+Selecting previously unselected package libcurl3-gnutls:i386.
+Preparing to unpack .../45-libcurl3-gnutls_7.57.0-1_i386.deb ...
+Unpacking libcurl3-gnutls:i386 (7.57.0-1) ...
+Selecting previously unselected package libgslcblas0:i386.
+Preparing to unpack .../46-libgslcblas0_2.4+dfsg-6_i386.deb ...
+Unpacking libgslcblas0:i386 (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl23:i386.
+Preparing to unpack .../47-libgsl23_2.4+dfsg-6_i386.deb ...
+Unpacking libgsl23:i386 (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl-dev.
+Preparing to unpack .../48-libgsl-dev_2.4+dfsg-6_i386.deb ...
+Unpacking libgsl-dev (2.4+dfsg-6) ...
+Selecting previously unselected package libhts2:i386.
+Preparing to unpack .../49-libhts2_1.5-6_i386.deb ...
+Unpacking libhts2:i386 (1.5-6) ...
+Selecting previously unselected package liblzma-dev:i386.
+Preparing to unpack .../50-liblzma-dev_5.2.2-1.3_i386.deb ...
+Unpacking liblzma-dev:i386 (5.2.2-1.3) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../51-tabix_1.5-6_i386.deb ...
+Unpacking tabix (1.5-6) ...
+Selecting previously unselected package libhts-dev:i386.
+Preparing to unpack .../52-libhts-dev_1.5-6_i386.deb ...
+Unpacking libhts-dev:i386 (1.5-6) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../53-libio-pty-perl_1%3a1.08-1.1+b4_i386.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b4) ...
+Selecting previously unselected package zlib1g-dev:i386.
+Preparing to unpack .../54-zlib1g-dev_1%3a1.2.8.dfsg-5_i386.deb ...
+Unpacking zlib1g-dev:i386 (1:1.2.8.dfsg-5) ...
+Selecting previously unselected package sbuild-build-depends-bcftools-dummy.
+Preparing to unpack .../55-sbuild-build-depends-bcftools-dummy_0.invalid.0_i386.deb ...
+Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Setting up libncurses5:i386 (6.0+20171125-1) ...
+Setting up libbz2-dev:i386 (1.0.6-8.1) ...
+Setting up libarchive-zip-perl (1.59-1) ...
+Setting up libnghttp2-14:i386 (1.28.0-1) ...
+Setting up libio-pty-perl (1:1.08-1.1+b4) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libsigsegv2:i386 (2.11-1) ...
+Setting up libldap-common (2.4.45+dfsg-1) ...
+Setting up libpsl5:i386 (0.19.1-4) ...
+Setting up groff-base (1.22.3-9) ...
+Setting up libglib2.0-0:i386 (2.54.2-1) ...
+No schema files found: doing nothing.
+Setting up libsasl2-modules-db:i386 (2.1.27~101-g0780600+dfsg-3) ...
+Setting up libsasl2-2:i386 (2.1.27~101-g0780600+dfsg-3) ...
+Setting up gettext-base (0.19.8.1-4) ...
+Setting up libpipeline1:i386 (1.5.0-1) ...
+Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-1+b1) ...
+Setting up m4 (1.4.18-1) ...
+Setting up libicu57:i386 (57.1-8) ...
+Setting up libbsd0:i386 (0.8.6-3) ...
+Setting up libxml2:i386 (2.9.4+dfsg1-5.1) ...
+Setting up libmagic-mgc (1:5.32-1) ...
+Setting up libmagic1:i386 (1:5.32-1) ...
+Setting up libcroco3:i386 (0.6.12-1) ...
+Setting up libssh2-1:i386 (1.8.0-1) ...
+Processing triggers for libc-bin (2.25-3) ...
+Setting up autotools-dev (20161112.1+nmu1) ...
+Setting up libldap-2.4-2:i386 (2.4.45+dfsg-1) ...
+Setting up libssl1.1:i386 (1.1.0g-2) ...
+Setting up liblzma-dev:i386 (5.2.2-1.3) ...
+Setting up libkeyutils1:i386 (1.5.9-9.2) ...
+Setting up bsdmainutils (9.0.14) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libgslcblas0:i386 (2.4+dfsg-6) ...
+Setting up autopoint (0.19.8.1-4) ...
+Setting up zlib1g-dev:i386 (1:1.2.8.dfsg-5) ...
+Setting up libfile-stripnondeterminism-perl (0.040-1) ...
+Setting up libgsl23:i386 (2.4+dfsg-6) ...
+Setting up gettext (0.19.8.1-4) ...
+Setting up libgsl-dev (2.4+dfsg-6) ...
+Setting up autoconf (2.69-11) ...
+Setting up file (1:5.32-1) ...
+Setting up libkrb5support0:i386 (1.15.2-2) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up automake (1:1.15.1-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
+Setting up man-db (2.7.6.1-4) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libtool (2.4.6-2) ...
+Setting up libk5crypto3:i386 (1.15.2-2) ...
+Setting up po-debconf (1.0.20) ...
+Setting up libkrb5-3:i386 (1.15.2-2) ...
+Setting up libgssapi-krb5-2:i386 (1.15.2-2) ...
+Setting up libcurl3-gnutls:i386 (7.57.0-1) ...
+Setting up tabix (1.5-6) ...
+Setting up libhts2:i386 (1.5-6) ...
+Setting up libhts-dev:i386 (1.5-6) ...
+Setting up dh-autoreconf (15) ...
+Setting up dh-strip-nondeterminism (0.040-1) ...
+Setting up debhelper (10.10.9) ...
+Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.25-3) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+
++------------------------------------------------------------------------------+
+| Build environment |
++------------------------------------------------------------------------------+
+
+Kernel: Linux 4.9.0-4-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.29.1-11 dpkg-dev_1.19.0.4 g++-7_7.2.0-17 gcc-7_7.2.0-17 libc6-dev_2.25-3 libstdc++-7-dev_7.2.0-17 libstdc++6_7.2.0-17 linux-libc-dev_4.14.2-1
+Package versions: adduser_3.116 apt_1.6~alpha5 aptitude_0.8.10-1 aptitude-common_0.8.10-1 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-11 binutils-common_2.29.1-11 binutils-i686-linux-gnu_2.29.1-11 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 coreutils_8.28-1 cpp_4:7.2.0-1d1 cpp-7_7.2.0-17 dash_0.5.8-2.5 debconf_1.5.65 debhelper_10.10.9 debian-archive-k [...]
+
++------------------------------------------------------------------------------+
+| Build |
++------------------------------------------------------------------------------+
+
+
+Unpack source
+-------------
+
+gpgv: unknown type of key resource 'trustedkeys.kbx'
+gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
+gpgv: Signature made Mon Dec 11 14:53:09 2017 UTC
+gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
+gpgv: issuer "tillea at rki.de"
+gpgv: Can't check signature: No public key
+dpkg-source: warning: failed to verify signature on ./bcftools_1.6-1.dsc
+dpkg-source: info: extracting bcftools in /<<PKGBUILDDIR>>
+dpkg-source: info: unpacking bcftools_1.6.orig.tar.gz
+dpkg-source: info: unpacking bcftools_1.6-1.debian.tar.xz
+dpkg-source: info: applying tests-pluginpath.patch
+dpkg-source: info: applying test-regidx-unsigned-char.patch
+dpkg-source: info: applying fix-test_vcf_query.patch
+
+Check disk space
+----------------
+
+Sufficient free space for build
+
+User Environment
+----------------
+
+APT_CONFIG=/var/lib/sbuild/apt.conf
+DEB_BUILD_OPTIONS=parallel=4
+HOME=/sbuild-nonexistent
+LC_ALL=POSIX
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=experimental-i386-sbuild
+SCHROOT_CHROOT_NAME=experimental-i386-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1009
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=experimental-i386-sbuild-6fc96d61-f17a-4ba5-a536-28f5e399237d
+SCHROOT_UID=2952
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
+XDG_RUNTIME_DIR=/run/user/2952
+XDG_SESSION_ID=1
+
+dpkg-buildpackage
+-----------------
+
+dpkg-buildpackage: info: source package bcftools
+dpkg-buildpackage: info: source version 1.6-1
+dpkg-buildpackage: info: source distribution experimental
+ dpkg-source --before-build bcftools-1.6
+dpkg-buildpackage: info: host architecture i386
+ fakeroot debian/rules clean
+rm -f config.mk && touch config.mk
+dh clean --parallel
+ dh_auto_clean
+ make -j4 distclean
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+rm -f test/*.o test/*~
+rm -f plugins/*.so plugins/*.P
+rm -rf plugins/*.dSYM
+rm -f gmon.out *.o *~ version.h plugins/*.so plugins/*.P
+rm -rf *.dSYM plugins/*.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 '/<<PKGBUILDDIR>>'
+ dh_clean
+ debian/rules build-arch
+dh build-arch --parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_autoreconf
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+rm -f config.mk && touch config.mk
+export MAKEFLAGS="-s"; dh_autoreconf
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+dh_auto_configure -- \
+--with-htslib=system \
+--enable-gsl \
+--with-cblas=gslcblas \
+--with-bcf-plugin-dir=/usr/lib/i386-linux-gnu/bcftools
+ ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/i386-linux-gnu/bcftools
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for 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... -ldl
+checking if the compiler accepts -rdynamic... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ dh_auto_build -a -O--parallel
+ make -j4
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+echo '#define BCFTOOLS_VERSION "1.6"' > version.h
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/i386-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c
+gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl
+gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -ldl -ldl
+gcc -rdynamic -pthread -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 vcfplugin.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 ccall.o em.o prob1.o kmin.o -l [...]
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ dh_auto_test -a -O--parallel
+ make -j4 test VERBOSE=1
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+./test/test-rbuf
+Inserted 1-9 starting at offset 5:
+ 5 6 7 8 9 0 1 2 3
+ 1 2 3 4 5 6 7 8 9
+4th is 4
+Deleting 1-2:
+ 7 8 9 0 1 2 3
+ 3 4 5 6 7 8 9
+Prepending 0-8:
+ 8 9 0 1 2 3 4 5 6 7
+ 8 7 6 5 4 3 2 1 0 3
+Expanding:
+ 8 9 10 11 12 13 14 15 16 17
+ 8 7 6 5 4 3 2 1 0 3
+./test/test-regidx
+REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix=
+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/E8DqbDVkFw/merge.a.vcf.gz 2:3199812-3199812
+.. ok
+
+test_tabix:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/E8DqbDVkFw/merge.a.bcf 2:3199812-3199812
+.. ok
+
+test_tabix:
+ tabix /tmp/E8DqbDVkFw/merge.a.vcf.gz 1:3000151-3000151
+.. ok
+
+test_tabix:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/E8DqbDVkFw/merge.a.bcf 1:3000151-3000151
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/E8DqbDVkFw/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/E8DqbDVkFw/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/E8DqbDVkFw/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/E8DqbDVkFw/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/E8DqbDVkFw/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/E8DqbDVkFw/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/E8DqbDVkFw/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/E8DqbDVkFw/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/E8DqbDVkFw/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/E8DqbDVkFw/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/E8DqbDVkFw/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/E8DqbDVkFw/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/E8DqbDVkFw/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/E8DqbDVkFw/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/E8DqbDVkFw/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/E8DqbDVkFw/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/E8DqbDVkFw/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/E8DqbDVkFw/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/E8DqbDVkFw/empty.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/E8DqbDVkFw/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/E8DqbDVkFw/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/E8DqbDVkFw/empty.bcf
+.. ok
+
+test_vcf_check:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/E8DqbDVkFw/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check_merge:
+ /<<PKGBUILDDIR>>/misc/plot-vcfstats -m /tmp/E8DqbDVkFw/check.1.chk /tmp/E8DqbDVkFw/check.2.chk /tmp/E8DqbDVkFw/check.3.chk /tmp/E8DqbDVkFw/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/E8DqbDVkFw/stats.a.vcf.gz /tmp/E8DqbDVkFw/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s B /tmp/E8DqbDVkFw/stats.a.vcf.gz /tmp/E8DqbDVkFw/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/E8DqbDVkFw/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 /tmp/E8DqbDVkFw/isec.a.vcf.gz /tmp/E8DqbDVkFw/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 /tmp/E8DqbDVkFw/isec.a.vcf.gz /tmp/E8DqbDVkFw/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/E8DqbDVkFw/isec.a.vcf.gz /tmp/E8DqbDVkFw/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/E8DqbDVkFw/isec.a.vcf.gz /tmp/E8DqbDVkFw/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -c both /tmp/E8DqbDVkFw/isec.a.vcf.gz /tmp/E8DqbDVkFw/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -c both /tmp/E8DqbDVkFw/isec.a.vcf.gz /tmp/E8DqbDVkFw/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -c any /tmp/E8DqbDVkFw/isec.a.vcf.gz /tmp/E8DqbDVkFw/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -c any /tmp/E8DqbDVkFw/isec.a.vcf.gz /tmp/E8DqbDVkFw/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -C -c any /tmp/E8DqbDVkFw/isec.a.vcf.gz /tmp/E8DqbDVkFw/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -C -c any /tmp/E8DqbDVkFw/isec.a.vcf.gz /tmp/E8DqbDVkFw/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec2:
+ /<<PKGBUILDDIR>>/bcftools isec --no-version -T /tmp/E8DqbDVkFw/isec.tab.gz /tmp/E8DqbDVkFw/isec.a.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec2:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -T /tmp/E8DqbDVkFw/isec.tab.gz /tmp/E8DqbDVkFw/isec.a.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples /tmp/E8DqbDVkFw/merge.a.vcf.gz /tmp/E8DqbDVkFw/merge.b.vcf.gz /tmp/E8DqbDVkFw/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.out
+ /<<PKGBUILDDIR>>/test/merge.abc.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples /tmp/E8DqbDVkFw/merge.a.vcf.gz /tmp/E8DqbDVkFw/merge.b.vcf.gz /tmp/E8DqbDVkFw/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.out
+ /<<PKGBUILDDIR>>/test/merge.abc.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -Fx /tmp/E8DqbDVkFw/merge.a.vcf.gz /tmp/E8DqbDVkFw/merge.b.vcf.gz /tmp/E8DqbDVkFw/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -Fx /tmp/E8DqbDVkFw/merge.a.vcf.gz /tmp/E8DqbDVkFw/merge.b.vcf.gz /tmp/E8DqbDVkFw/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -0 /tmp/E8DqbDVkFw/merge.a.vcf.gz /tmp/E8DqbDVkFw/merge.b.vcf.gz /tmp/E8DqbDVkFw/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -0 /tmp/E8DqbDVkFw/merge.a.vcf.gz /tmp/E8DqbDVkFw/merge.b.vcf.gz /tmp/E8DqbDVkFw/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m none /tmp/E8DqbDVkFw/merge.2.a.vcf.gz /tmp/E8DqbDVkFw/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.none.out
+ /<<PKGBUILDDIR>>/test/merge.2.none.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m none /tmp/E8DqbDVkFw/merge.2.a.vcf.gz /tmp/E8DqbDVkFw/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.none.out
+ /<<PKGBUILDDIR>>/test/merge.2.none.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m both /tmp/E8DqbDVkFw/merge.2.a.vcf.gz /tmp/E8DqbDVkFw/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.both.out
+ /<<PKGBUILDDIR>>/test/merge.2.both.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m both /tmp/E8DqbDVkFw/merge.2.a.vcf.gz /tmp/E8DqbDVkFw/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.both.out
+ /<<PKGBUILDDIR>>/test/merge.2.both.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m all /tmp/E8DqbDVkFw/merge.2.a.vcf.gz /tmp/E8DqbDVkFw/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.all.out
+ /<<PKGBUILDDIR>>/test/merge.2.all.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m all /tmp/E8DqbDVkFw/merge.2.a.vcf.gz /tmp/E8DqbDVkFw/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.all.out
+ /<<PKGBUILDDIR>>/test/merge.2.all.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/E8DqbDVkFw/merge.3.a.vcf.gz /tmp/E8DqbDVkFw/merge.3.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.3.out
+ /<<PKGBUILDDIR>>/test/merge.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/E8DqbDVkFw/merge.3.a.vcf.gz /tmp/E8DqbDVkFw/merge.3.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.3.out
+ /<<PKGBUILDDIR>>/test/merge.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m id /tmp/E8DqbDVkFw/merge.4.a.vcf.gz /tmp/E8DqbDVkFw/merge.4.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.4.out
+ /<<PKGBUILDDIR>>/test/merge.4.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m id /tmp/E8DqbDVkFw/merge.4.a.vcf.gz /tmp/E8DqbDVkFw/merge.4.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.4.out
+ /<<PKGBUILDDIR>>/test/merge.4.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - /tmp/E8DqbDVkFw/gvcf.merge.1.vcf.gz /tmp/E8DqbDVkFw/gvcf.merge.2.vcf.gz /tmp/E8DqbDVkFw/gvcf.merge.3.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - /tmp/E8DqbDVkFw/gvcf.merge.1.vcf.gz /tmp/E8DqbDVkFw/gvcf.merge.2.vcf.gz /tmp/E8DqbDVkFw/gvcf.merge.3.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - /tmp/E8DqbDVkFw/merge.gvcf.2.a.vcf.gz /tmp/E8DqbDVkFw/merge.gvcf.2.b.vcf.gz /tmp/E8DqbDVkFw/merge.gvcf.2.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - /tmp/E8DqbDVkFw/merge.gvcf.2.a.vcf.gz /tmp/E8DqbDVkFw/merge.gvcf.2.b.vcf.gz /tmp/E8DqbDVkFw/merge.gvcf.2.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - -i SRC:join /tmp/E8DqbDVkFw/merge.gvcf.3.a.vcf.gz /tmp/E8DqbDVkFw/merge.gvcf.3.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/E8DqbDVkFw/merge.gvcf.3.a.vcf.gz /tmp/E8DqbDVkFw/merge.gvcf.3.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version /tmp/E8DqbDVkFw/merge.5.a.vcf.gz /tmp/E8DqbDVkFw/merge.5.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob /tmp/E8DqbDVkFw/merge.5.a.vcf.gz /tmp/E8DqbDVkFw/merge.5.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/E8DqbDVkFw/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XRI\n' -i'XRI[*]>1111'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' /tmp/E8DqbDVkFw/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/E8DqbDVkFw/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/E8DqbDVkFw/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10' /tmp/E8DqbDVkFw/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/E8DqbDVkFw/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/E8DqbDVkFw/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/E8DqbDVkFw/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/E8DqbDVkFw/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/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/E8DqbDVkFw/view.vectors.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/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:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' /tmp/E8DqbDVkFw/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' /tmp/E8DqbDVkFw/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' /tmp/E8DqbDVkFw/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' /tmp/E8DqbDVkFw/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/E8DqbDVkFw/query.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%LINE' /tmp/E8DqbDVkFw/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%LINE'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/E8DqbDVkFw/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/E8DqbDVkFw/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/E8DqbDVkFw/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/E8DqbDVkFw/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/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/E8DqbDVkFw/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/filter-missing-floats.vcf.gz | /<<PKGBUILDDIR>>/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:
+ /<<PKGBUILDDIR>>/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/E8DqbDVkFw/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/filter-missing-floats.vcf.gz | /<<PKGBUILDDIR>>/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:
+ /<<PKGBUILDDIR>>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/E8DqbDVkFw/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/E8DqbDVkFw/query.filter.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/query.filter.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5'
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -cx -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/E8DqbDVkFw/norm.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -cx -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/E8DqbDVkFw/norm.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- /tmp/E8DqbDVkFw/norm.split.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.split.out
+ /<<PKGBUILDDIR>>/test/norm.split.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- /tmp/E8DqbDVkFw/norm.split.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.split.out
+ /<<PKGBUILDDIR>>/test/norm.split.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- /tmp/E8DqbDVkFw/norm.split.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- /tmp/E8DqbDVkFw/norm.split.2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/E8DqbDVkFw/norm.split.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.split.and.norm.out
+ /<<PKGBUILDDIR>>/test/norm.split.and.norm.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/E8DqbDVkFw/norm.split.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.split.and.norm.out
+ /<<PKGBUILDDIR>>/test/norm.split.and.norm.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/E8DqbDVkFw/norm.merge.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.out
+ /<<PKGBUILDDIR>>/test/norm.merge.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/E8DqbDVkFw/norm.merge.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.out
+ /<<PKGBUILDDIR>>/test/norm.merge.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/E8DqbDVkFw/norm.merge.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/E8DqbDVkFw/norm.merge.2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/E8DqbDVkFw/norm.merge.3.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.3.out
+ /<<PKGBUILDDIR>>/test/norm.merge.3.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/E8DqbDVkFw/norm.merge.3.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.'
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.3.out
+ /<<PKGBUILDDIR>>/test/norm.merge.3.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ -s /tmp/E8DqbDVkFw/norm.merge.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ -s /tmp/E8DqbDVkFw/norm.merge.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -Nc s -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/E8DqbDVkFw/norm.setref.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -Nc s -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/E8DqbDVkFw/norm.setref.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/E8DqbDVkFw/norm.telomere.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/E8DqbDVkFw/norm.telomere.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/E8DqbDVkFw/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/E8DqbDVkFw/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/E8DqbDVkFw/view.vcf.gz -r20,Y
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/E8DqbDVkFw/view.vcf.gz -r20,Y | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -xs NA00003 /tmp/E8DqbDVkFw/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -xs NA00003 /tmp/E8DqbDVkFw/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/E8DqbDVkFw/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/E8DqbDVkFw/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -p /tmp/E8DqbDVkFw/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -p /tmp/E8DqbDVkFw/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -P /tmp/E8DqbDVkFw/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -P /tmp/E8DqbDVkFw/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/E8DqbDVkFw/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/E8DqbDVkFw/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -Hu /tmp/E8DqbDVkFw/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -GVsnps /tmp/E8DqbDVkFw/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -GVsnps /tmp/E8DqbDVkFw/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/E8DqbDVkFw/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/E8DqbDVkFw/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -s ^NA00003 /tmp/E8DqbDVkFw/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -s ^NA00003 /tmp/E8DqbDVkFw/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version /tmp/E8DqbDVkFw/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/view.omitgenotypes.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -G /tmp/E8DqbDVkFw/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -G /tmp/E8DqbDVkFw/view.omitgenotypes.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -HG /tmp/E8DqbDVkFw/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -a /tmp/E8DqbDVkFw/many.alleles.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -a /tmp/E8DqbDVkFw/many.alleles.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asA /tmp/E8DqbDVkFw/view.vectors.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asA /tmp/E8DqbDVkFw/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asB /tmp/E8DqbDVkFw/view.vectors.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asB /tmp/E8DqbDVkFw/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asA /tmp/E8DqbDVkFw/view.vectors.2.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asA /tmp/E8DqbDVkFw/view.vectors.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[0]="AAAAAA"' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[2]="C"' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[4]="EE"' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FRS[1]="BB"' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'TXT0="text"' /tmp/E8DqbDVkFw/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -T /<<PKGBUILDDIR>>/test/view.chrs.tab /tmp/E8DqbDVkFw/view.chrs.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -T /<<PKGBUILDDIR>>/test/view.chrs.tab /tmp/E8DqbDVkFw/view.chrs.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -i 'POS>=3062917' /tmp/E8DqbDVkFw/filter.2.vcf.gz 1:3062917-3157410
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -i 'POS>=3062917' /tmp/E8DqbDVkFw/filter.2.vcf.gz 1:3062917-3157410 | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'TXT0="text"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'TXT0="text"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FRS[1]="BB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FRS[1]="BB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[0]="AAAAAA"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[0]="AAAAAA"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[1]="BBB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[1]="BBB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[4]="EE"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[4]="EE"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/STR="XX"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/STR="XX"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -C5:nonmajor /tmp/E8DqbDVkFw/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -c6:nonmajor /tmp/E8DqbDVkFw/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -q0.3:major /tmp/E8DqbDVkFw/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/E8DqbDVkFw/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/E8DqbDVkFw/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/E8DqbDVkFw/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mg0 /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mg0 /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call_cAls:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mA -C alleles -T /tmp/E8DqbDVkFw/mpileup.tab.gz /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call_cAls:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mA -C alleles -T /tmp/E8DqbDVkFw/mpileup.tab.gz /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv /<<PKGBUILDDIR>>/test/mpileup.c.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv /<<PKGBUILDDIR>>/test/mpileup.c.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -mx -g2 -G2 /<<PKGBUILDDIR>>/test/filter.1.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -mx -g2 -G2 /<<PKGBUILDDIR>>/test/filter.1.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<<PKGBUILDDIR>>/test/filter.2.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'ALT="."' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'ALT="."' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S . -i 'FORMAT/TEST3<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S . -i 'FORMAT/TEST4<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="A"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="A"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="RR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="RR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="RA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="RA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="AR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="AR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="AA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="AA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="aA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="aA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="Aa"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="Aa"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HOM"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HOM"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HET"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HET"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HAP"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HAP"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -m 0 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.WXeuEH
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -Ob -m 0 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.bmFslI
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -m 1000 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.2sV42K
+Merging 3 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -Ob -m 1000 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.ZrnoGL
+Merging 3 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<<PKGBUILDDIR>>/test/regions.tab /tmp/E8DqbDVkFw/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<<PKGBUILDDIR>>/test/regions.tab
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /<<PKGBUILDDIR>>/test/regions.tab /tmp/E8DqbDVkFw/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/E8DqbDVkFw/regions.tab.gz /tmp/E8DqbDVkFw/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/E8DqbDVkFw/regions.tab.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/E8DqbDVkFw/regions.tab.gz /tmp/E8DqbDVkFw/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/E8DqbDVkFw/regions.bed /tmp/E8DqbDVkFw/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/E8DqbDVkFw/regions.bed
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/E8DqbDVkFw/regions.bed /tmp/E8DqbDVkFw/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/E8DqbDVkFw/regions.bed.gz /tmp/E8DqbDVkFw/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/E8DqbDVkFw/regions.bed.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/E8DqbDVkFw/regions.bed.gz /tmp/E8DqbDVkFw/regions.vcf.gz
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/E8DqbDVkFw/annotate.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/E8DqbDVkFw/annotate.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/E8DqbDVkFw/annotate2.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/E8DqbDVkFw/annotate2.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/E8DqbDVkFw/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/E8DqbDVkFw/annotate.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/E8DqbDVkFw/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/E8DqbDVkFw/annotate.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/E8DqbDVkFw/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/E8DqbDVkFw/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/annotate4.out
+ /<<PKGBUILDDIR>>/test/annotate4.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/E8DqbDVkFw/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/E8DqbDVkFw/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/annotate4.out
+ /<<PKGBUILDDIR>>/test/annotate4.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/E8DqbDVkFw/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/E8DqbDVkFw/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/E8DqbDVkFw/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/E8DqbDVkFw/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -x FORMAT /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -x FORMAT /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/E8DqbDVkFw/annots4.vcf.gz -c +INFO /tmp/E8DqbDVkFw/annotate4.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/annotate8.out
+ /<<PKGBUILDDIR>>/test/annotate8.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/E8DqbDVkFw/annots4.vcf.gz -c +INFO /tmp/E8DqbDVkFw/annotate4.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/annotate8.out
+ /<<PKGBUILDDIR>>/test/annotate8.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/E8DqbDVkFw/annots4.tab.gz -h /<<PKGBUILDDIR>>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<<PKGBUILDDIR>>/test/annotate4.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/annotate8.out
+ /<<PKGBUILDDIR>>/test/annotate8.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/E8DqbDVkFw/annots4.tab.gz -h /<<PKGBUILDDIR>>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<<PKGBUILDDIR>>/test/annotate4.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/annotate8.out
+ /<<PKGBUILDDIR>>/test/annotate8.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/E8DqbDVkFw/annots10.tab.gz -h /<<PKGBUILDDIR>>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<<PKGBUILDDIR>>/test/annotate10.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/annotate10.out
+ /<<PKGBUILDDIR>>/test/annotate10.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/E8DqbDVkFw/annots10.tab.gz -h /<<PKGBUILDDIR>>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<<PKGBUILDDIR>>/test/annotate10.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/annotate10.out
+ /<<PKGBUILDDIR>>/test/annotate10.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/E8DqbDVkFw/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/E8DqbDVkFw/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/annotate11.out
+ /<<PKGBUILDDIR>>/test/annotate11.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/E8DqbDVkFw/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/E8DqbDVkFw/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/annotate11.out
+ /<<PKGBUILDDIR>>/test/annotate11.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/E8DqbDVkFw/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<<PKGBUILDDIR>>/test/annotate2.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/annotate11.out
+ /<<PKGBUILDDIR>>/test/annotate11.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/E8DqbDVkFw/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<<PKGBUILDDIR>>/test/annotate2.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/annotate11.out
+ /<<PKGBUILDDIR>>/test/annotate11.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/E8DqbDVkFw/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/E8DqbDVkFw/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/E8DqbDVkFw/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/E8DqbDVkFw/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/E8DqbDVkFw/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/E8DqbDVkFw/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/E8DqbDVkFw/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/E8DqbDVkFw/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +missing2ref --no-version /tmp/E8DqbDVkFw/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +missing2ref --no-version /tmp/E8DqbDVkFw/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/E8DqbDVkFw/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/E8DqbDVkFw/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/E8DqbDVkFw/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/E8DqbDVkFw/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/E8DqbDVkFw/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<<PKGBUILDDIR>>/test/annotate9.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/E8DqbDVkFw/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<<PKGBUILDDIR>>/test/annotate9.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-AN-AC --no-version /tmp/E8DqbDVkFw/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-AN-AC --no-version /tmp/E8DqbDVkFw/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +dosage /tmp/E8DqbDVkFw/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +dosage /tmp/E8DqbDVkFw/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixploidy --no-version /tmp/E8DqbDVkFw/fixploidy.vcf.gz -- -s /<<PKGBUILDDIR>>/test/fixploidy.samples -p /<<PKGBUILDDIR>>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixploidy --no-version /tmp/E8DqbDVkFw/fixploidy.bcf -- -s /<<PKGBUILDDIR>>/test/fixploidy.samples -p /<<PKGBUILDDIR>>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/E8DqbDVkFw/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/E8DqbDVkFw/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/E8DqbDVkFw/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/guess-ploidy.GL.out
+ /<<PKGBUILDDIR>>/test/guess-ploidy.GL.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/E8DqbDVkFw/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/guess-ploidy.GL.out
+ /<<PKGBUILDDIR>>/test/guess-ploidy.GL.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/E8DqbDVkFw/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/E8DqbDVkFw/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/E8DqbDVkFw/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/E8DqbDVkFw/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/E8DqbDVkFw/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/E8DqbDVkFw/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/E8DqbDVkFw/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/E8DqbDVkFw/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/E8DqbDVkFw/view.vcf.gz -- -t AC -S /<<PKGBUILDDIR>>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/E8DqbDVkFw/view.bcf -- -t AC -S /<<PKGBUILDDIR>>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/E8DqbDVkFw/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/E8DqbDVkFw/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/E8DqbDVkFw/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/E8DqbDVkFw/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/E8DqbDVkFw/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +trio-switch-rate /tmp/E8DqbDVkFw/trio.vcf.gz -- -p /<<PKGBUILDDIR>>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +trio-switch-rate /tmp/E8DqbDVkFw/trio.bcf -- -p /<<PKGBUILDDIR>>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +ad-bias /tmp/E8DqbDVkFw/ad-bias.vcf.gz -- -s /<<PKGBUILDDIR>>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +ad-bias /tmp/E8DqbDVkFw/ad-bias.bcf -- -s /<<PKGBUILDDIR>>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +af-dist /tmp/E8DqbDVkFw/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +af-dist /tmp/E8DqbDVkFw/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixref /tmp/E8DqbDVkFw/fixref.2a.vcf.gz -- -f /<<PKGBUILDDIR>>/test/norm.fa -i /tmp/E8DqbDVkFw/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixref /tmp/E8DqbDVkFw/fixref.2a.bcf -- -f /<<PKGBUILDDIR>>/test/norm.fa -i /tmp/E8DqbDVkFw/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/E8DqbDVkFw/aa.vcf.gz -- -f /<<PKGBUILDDIR>>/test/aa.fa -c AA -h /<<PKGBUILDDIR>>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/E8DqbDVkFw/aa.bcf -- -f /<<PKGBUILDDIR>>/test/aa.fa -c AA -h /<<PKGBUILDDIR>>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/E8DqbDVkFw/ref.vcf.gz -- -f /<<PKGBUILDDIR>>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/E8DqbDVkFw/ref.bcf -- -f /<<PKGBUILDDIR>>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/E8DqbDVkFw/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/E8DqbDVkFw/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/E8DqbDVkFw/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/E8DqbDVkFw/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/E8DqbDVkFw/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/E8DqbDVkFw/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/E8DqbDVkFw/mendelian.vcf.gz -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/E8DqbDVkFw/mendelian.bcf -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/E8DqbDVkFw/mendelian.vcf.gz -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/E8DqbDVkFw/mendelian.bcf -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/E8DqbDVkFw/mendelian.vcf.gz -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/E8DqbDVkFw/mendelian.bcf -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version /tmp/E8DqbDVkFw/concat.1.a.vcf.gz /tmp/E8DqbDVkFw/concat.1.b.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob /tmp/E8DqbDVkFw/concat.1.a.vcf.gz /tmp/E8DqbDVkFw/concat.1.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version /tmp/E8DqbDVkFw/concat.1.a.bcf /tmp/E8DqbDVkFw/concat.1.b.bcf
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob /tmp/E8DqbDVkFw/concat.1.a.bcf /tmp/E8DqbDVkFw/concat.1.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -a /tmp/E8DqbDVkFw/concat.2.a.vcf.gz /tmp/E8DqbDVkFw/concat.2.b.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -a /tmp/E8DqbDVkFw/concat.2.a.vcf.gz /tmp/E8DqbDVkFw/concat.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -a /tmp/E8DqbDVkFw/concat.2.a.bcf /tmp/E8DqbDVkFw/concat.2.b.bcf
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -a /tmp/E8DqbDVkFw/concat.2.a.bcf /tmp/E8DqbDVkFw/concat.2.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -aD /tmp/E8DqbDVkFw/concat.2.a.vcf.gz /tmp/E8DqbDVkFw/concat.2.b.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -aD /tmp/E8DqbDVkFw/concat.2.a.vcf.gz /tmp/E8DqbDVkFw/concat.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -aD /tmp/E8DqbDVkFw/concat.2.a.bcf /tmp/E8DqbDVkFw/concat.2.b.bcf
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -aD /tmp/E8DqbDVkFw/concat.2.a.bcf /tmp/E8DqbDVkFw/concat.2.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -l /tmp/E8DqbDVkFw/concat.3.a.vcf.gz /tmp/E8DqbDVkFw/concat.3.b.vcf.gz /tmp/E8DqbDVkFw/concat.3.0.vcf.gz /tmp/E8DqbDVkFw/concat.3.c.vcf.gz /tmp/E8DqbDVkFw/concat.3.d.vcf.gz /tmp/E8DqbDVkFw/concat.3.e.vcf.gz /tmp/E8DqbDVkFw/concat.3.f.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -l /tmp/E8DqbDVkFw/concat.3.a.vcf.gz /tmp/E8DqbDVkFw/concat.3.b.vcf.gz /tmp/E8DqbDVkFw/concat.3.0.vcf.gz /tmp/E8DqbDVkFw/concat.3.c.vcf.gz /tmp/E8DqbDVkFw/concat.3.d.vcf.gz /tmp/E8DqbDVkFw/concat.3.e.vcf.gz /tmp/E8DqbDVkFw/concat.3.f.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -l /tmp/E8DqbDVkFw/concat.3.a.bcf /tmp/E8DqbDVkFw/concat.3.b.bcf /tmp/E8DqbDVkFw/concat.3.0.bcf /tmp/E8DqbDVkFw/concat.3.c.bcf /tmp/E8DqbDVkFw/concat.3.d.bcf /tmp/E8DqbDVkFw/concat.3.e.bcf /tmp/E8DqbDVkFw/concat.3.f.bcf
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -l /tmp/E8DqbDVkFw/concat.3.a.bcf /tmp/E8DqbDVkFw/concat.3.b.bcf /tmp/E8DqbDVkFw/concat.3.0.bcf /tmp/E8DqbDVkFw/concat.3.c.bcf /tmp/E8DqbDVkFw/concat.3.d.bcf /tmp/E8DqbDVkFw/concat.3.e.bcf /tmp/E8DqbDVkFw/concat.3.f.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Random seed for test_naive_concat: 447810544
+.. ok
+
+test_naive_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --naive /tmp/E8DqbDVkFw/naive_concat.0.bcf /tmp/E8DqbDVkFw/naive_concat.1.bcf /tmp/E8DqbDVkFw/naive_concat.2.bcf /tmp/E8DqbDVkFw/naive_concat.3.bcf /tmp/E8DqbDVkFw/naive_concat.4.bcf /tmp/E8DqbDVkFw/naive_concat.5.bcf /tmp/E8DqbDVkFw/naive_concat.6.bcf /tmp/E8DqbDVkFw/naive_concat.7.bcf /tmp/E8DqbDVkFw/naive_concat.8.bcf /tmp/E8DqbDVkFw/naive_concat.9.bcf | /<<PKGBUILDDIR>>/bcftools view -H
+.. ok
+
+test_naive_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --naive /tmp/E8DqbDVkFw/naive_concat.0.vcf.gz /tmp/E8DqbDVkFw/naive_concat.1.vcf.gz /tmp/E8DqbDVkFw/naive_concat.2.vcf.gz /tmp/E8DqbDVkFw/naive_concat.3.vcf.gz /tmp/E8DqbDVkFw/naive_concat.4.vcf.gz /tmp/E8DqbDVkFw/naive_concat.5.vcf.gz /tmp/E8DqbDVkFw/naive_concat.6.vcf.gz /tmp/E8DqbDVkFw/naive_concat.7.vcf.gz /tmp/E8DqbDVkFw/naive_concat.8.vcf.gz /tmp/E8DqbDVkFw/naive_concat.9.vcf.gz | /<<PKGBUILDDIR>>/bcftools view -H
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /tmp/E8DqbDVkFw/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/E8DqbDVkFw/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /tmp/E8DqbDVkFw/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/E8DqbDVkFw/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /tmp/E8DqbDVkFw/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/E8DqbDVkFw/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /tmp/E8DqbDVkFw/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/E8DqbDVkFw/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /tmp/E8DqbDVkFw/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/E8DqbDVkFw/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /tmp/E8DqbDVkFw/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/E8DqbDVkFw/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /tmp/E8DqbDVkFw/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/E8DqbDVkFw/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /tmp/E8DqbDVkFw/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/E8DqbDVkFw/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /tmp/E8DqbDVkFw/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/E8DqbDVkFw/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /tmp/E8DqbDVkFw/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/E8DqbDVkFw/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /<<PKGBUILDDIR>>/test/empty.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/empty.vcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /tmp/E8DqbDVkFw/empty.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/E8DqbDVkFw/empty.bcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /tmp/E8DqbDVkFw/empty.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/E8DqbDVkFw/empty.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/E8DqbDVkFw/rename.map -Ov /tmp/E8DqbDVkFw/annotate.bcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/E8DqbDVkFw/rename.map -Ob /tmp/E8DqbDVkFw/annotate.bcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/E8DqbDVkFw/rename.map -Ov /<<PKGBUILDDIR>>/test/annotate.vcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/E8DqbDVkFw/rename.map -Ob /<<PKGBUILDDIR>>/test/annotate.vcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. /tmp/E8DqbDVkFw/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- /tmp/E8DqbDVkFw/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --tag PL /tmp/E8DqbDVkFw/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --tag PL /tmp/E8DqbDVkFw/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --vcf-ids /tmp/E8DqbDVkFw/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --vcf-ids /tmp/E8DqbDVkFw/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom /tmp/E8DqbDVkFw/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom /tmp/E8DqbDVkFw/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom --vcf-ids /tmp/E8DqbDVkFw/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom --vcf-ids /tmp/E8DqbDVkFw/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h -,.,. /tmp/E8DqbDVkFw/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h -,.,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h .,-,. /tmp/E8DqbDVkFw/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h .,-,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h .,.,- /tmp/E8DqbDVkFw/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h .,.,- 2>/dev/null
+.. ok
+
+test_vcf_convert_hls2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -H /<<PKGBUILDDIR>>/test/convert.hls.gt.hap,/<<PKGBUILDDIR>>/test/convert.hls.gt.legend,/<<PKGBUILDDIR>>/test/convert.hls.gt.samples 2>/dev/null | grep -v ^##
+.. ok
+
+test_vcf_convert_hls2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -H /<<PKGBUILDDIR>>/test/convert.hls.gt.hap,/<<PKGBUILDDIR>>/test/convert.hls.gt.legend,/<<PKGBUILDDIR>>/test/convert.hls.gt.samples -Ou 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##
+.. ok
+
+test_vcf_convert_hs2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample2vcf /<<PKGBUILDDIR>>/test/convert.hs.gt.hap,/<<PKGBUILDDIR>>/test/convert.hs.gt.samples 2>/dev/null | grep -v ^##
+.. ok
+
+test_vcf_convert_hs2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample2vcf /<<PKGBUILDDIR>>/test/convert.hs.gt.hap,/<<PKGBUILDDIR>>/test/convert.hs.gt.samples -Ou 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample -,. /tmp/E8DqbDVkFw/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --hapsample -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample .,- /tmp/E8DqbDVkFw/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --hapsample .,- 2>/dev/null
+.. ok
+
+test_vcf_convert_gvcf:
+ /<<PKGBUILDDIR>>/bcftools convert --no-version --gvcf2vcf -f /<<PKGBUILDDIR>>/test/gvcf.fa /tmp/E8DqbDVkFw/convert.gvcf.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert_gvcf:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/E8DqbDVkFw/convert.gvcf.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --gvcf2vcf -f /<<PKGBUILDDIR>>/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools
+.. ok
+
+test_vcf_convert_tsv2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /<<PKGBUILDDIR>>/test/23andme.fa --tsv2vcf /<<PKGBUILDDIR>>/test/convert.23andme 2>/dev/null
+.. ok
+
+test_vcf_convert_tsv2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /<<PKGBUILDDIR>>/test/23andme.fa --tsv2vcf /<<PKGBUILDDIR>>/test/convert.23andme 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/E8DqbDVkFw/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/E8DqbDVkFw/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/E8DqbDVkFw/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/E8DqbDVkFw/consensus.1.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/E8DqbDVkFw/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/E8DqbDVkFw/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/E8DqbDVkFw/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/E8DqbDVkFw/consensus.2.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/E8DqbDVkFw/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -I -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/E8DqbDVkFw/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -I -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/E8DqbDVkFw/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/E8DqbDVkFw/consensus.3.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/E8DqbDVkFw/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/E8DqbDVkFw/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -c /tmp/E8DqbDVkFw/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/E8DqbDVkFw/consensus.4.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/E8DqbDVkFw/consensus2.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus2.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/E8DqbDVkFw/consensus2.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus2.fa -H 2 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/E8DqbDVkFw/empty.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa 2>/dev/null
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -b /tmp/E8DqbDVkFw/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/E8DqbDVkFw/mpileup.bam.urllist 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -b /tmp/E8DqbDVkFw/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/E8DqbDVkFw/mpileup.cram.urllist 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.out
+ /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.out
+ /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.out
+ /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.out
+ /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.out.new
+.. failed ...
+
+test_csq:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq.fa -g /<<PKGBUILDDIR>>/test/csq.gff3 /<<PKGBUILDDIR>>/test/csq.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq.gff3 ...
+Indexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ambiguous.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.gff /<<PKGBUILDDIR>>/test/csq/ENST00000593942/last-codon-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.gff ...
+Indexed 1 transcripts, 7 exons, 4 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.gff /<<PKGBUILDDIR>>/test/csq/ENST00000557788/long-overlap-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.gff /<<PKGBUILDDIR>>/test/csq/ENST00000545279/splice-region-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.gff ...
+Indexed 1 transcripts, 9 exons, 7 CDSs, 4 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff /<<PKGBUILDDIR>>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff /<<PKGBUILDDIR>>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff /<<PKGBUILDDIR>>/test/csq/ENST00000542803/splice-region.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff /<<PKGBUILDDIR>>/test/csq/ENST00000542803/splice-region.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff /<<PKGBUILDDIR>>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff /<<PKGBUILDDIR>>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.gff /<<PKGBUILDDIR>>/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.gff ...
+Indexed 1 transcripts, 7 exons, 6 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520868/long-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520795/long-inside-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520795/long-inside-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.gff /<<PKGBUILDDIR>>/test/csq/ENST00000519442/synon-splice-region-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff /<<PKGBUILDDIR>>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff /<<PKGBUILDDIR>>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.gff /<<PKGBUILDDIR>>/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.gff ...
+Indexed 1 transcripts, 26 exons, 26 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.gff /<<PKGBUILDDIR>>/test/csq/ENST00000436063/insert-before-utr.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.gff ...
+Indexed 1 transcripts, 7 exons, 7 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/snps.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/snps.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/insert3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/insert3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.gff /<<PKGBUILDDIR>>/test/csq/ENST00000420670/start-stop-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.gff ...
+Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.gff /<<PKGBUILDDIR>>/test/csq/ENST00000413103/long-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.gff ...
+Indexed 1 transcripts, 2 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.gff /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.gff /<<PKGBUILDDIR>>/test/csq/ENST00000409523/long-overlapping-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.gff /<<PKGBUILDDIR>>/test/csq/ENST00000390520/deletion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.gff /<<PKGBUILDDIR>>/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.gff /<<PKGBUILDDIR>>/test/csq/ENST00000381157/haploid-diploid.vcf | /<<PKGBUILDDIR>>/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 0 UTRs
+Calling...
+Warning: Skipping site with non-diploid/non-haploid genotypes at X:31180 C>T
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff /<<PKGBUILDDIR>>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff /<<PKGBUILDDIR>>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.gff /<<PKGBUILDDIR>>/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff /<<PKGBUILDDIR>>/test/csq/ENST00000373833/boundary-insertion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff /<<PKGBUILDDIR>>/test/csq/ENST00000373833/boundary-insertion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.gff /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.gff /<<PKGBUILDDIR>>/test/csq/ENST00000357367/stop-retained.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.gff ...
+Indexed 1 transcripts, 4 exons, 3 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff /<<PKGBUILDDIR>>/test/csq/ENST00000329454/boundary-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff /<<PKGBUILDDIR>>/test/csq/ENST00000329454/boundary-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff /<<PKGBUILDDIR>>/test/csq/ENST00000318249/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff /<<PKGBUILDDIR>>/test/csq/ENST00000318249/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff /<<PKGBUILDDIR>>/test/csq/ENST00000303039/not-a-stop.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff /<<PKGBUILDDIR>>/test/csq/ENST00000303039/not-a-stop.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.gff /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.gff ...
+Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff /<<PKGBUILDDIR>>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff /<<PKGBUILDDIR>>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff /<<PKGBUILDDIR>>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff /<<PKGBUILDDIR>>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.gff /<<PKGBUILDDIR>>/test/csq/ENST00000256452/intron.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.gff ...
+Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.gff /<<PKGBUILDDIR>>/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff /<<PKGBUILDDIR>>/test/csq/ENST00000218032/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff /<<PKGBUILDDIR>>/test/csq/ENST00000218032/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.fa -g /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.gff /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/synon.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.gff ...
+Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs
+Calling...
+.. ok
+
+
+Number of tests:
+ total .. 728
+ passed .. 662
+ failed .. 66
+
+Makefile:246: recipe for target 'test-plugins' failed
+make[1]: *** [test-plugins] Error 1
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+dh_auto_test: make -j4 test VERBOSE=1 returned exit code 2
+debian/rules:7: recipe for target 'build-arch' failed
+make: *** [build-arch] Error 2
+dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
+--------------------------------------------------------------------------------
+Build finished at 2017-12-11T16:15:52Z
+
+Finished
+--------
+
+
++------------------------------------------------------------------------------+
+| Cleanup |
++------------------------------------------------------------------------------+
+
+Purging /<<BUILDDIR>>
+Not cleaning session: cloned chroot in use
+E: Build failure (dpkg-buildpackage died)
+
++------------------------------------------------------------------------------+
+| Summary |
++------------------------------------------------------------------------------+
+
+Build Architecture: i386
+Build Type: any
+Build-Space: 21668
+Build-Time: 56
+Distribution: experimental
+Fail-Stage: build
+Host Architecture: i386
+Install-Time: 25
+Job: bcftools_1.6-1
+Machine Architecture: amd64
+Package: bcftools
+Package-Time: 98
+Source-Version: 1.6-1
+Space: 21668
+Status: attempted
+Version: 1.6-1
+--------------------------------------------------------------------------------
+Finished at 2017-12-11T16:15:52Z
+Build needed 00:01:38, 21668k disk space
diff --git a/bcftools_1.6-1_kfreebsd-i386.log b/bcftools_1.6-1_kfreebsd-i386.log
new file mode 100644
index 0000000..9f51db0
--- /dev/null
+++ b/bcftools_1.6-1_kfreebsd-i386.log
@@ -0,0 +1,4294 @@
+
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on fils.debian.org
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ bcftools 1.6-1 (kfreebsd-i386) 11 Dec 2017 16:21 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: bcftools
+Version: 1.6-1
+Source Version: 1.6-1
+Distribution: experimental
+Machine Architecture: kfreebsd-i386
+Host Architecture: kfreebsd-i386
+Build Architecture: kfreebsd-i386
+
+I: NOTICE: Log filtering will replace 'build/bcftools-mVNtLt/bcftools-1.6' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/bcftools-mVNtLt' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/experimental-k-i-sbuild-1513009279-42128' with '«CHROOT»'
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Get:1 http://ftp.debian.org/debian unstable InRelease [240 kB]
+Get:2 http://ftp.de.debian.org/debian unstable InRelease [240 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:4 http://ftp.debian.org/debian experimental InRelease [107 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-experimental InRelease [58.9 kB]
+Get:6 http://ftp.de.debian.org/debian experimental InRelease [107 kB]
+Get:7 http://ftp.debian.org/debian unstable/contrib Sources [50.5 kB]
+Get:8 http://ftp.debian.org/debian unstable/non-free Sources [83.9 kB]
+Get:9 http://ftp.debian.org/debian unstable/main Sources [7953 kB]
+Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [123 kB]
+Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1916 B]
+Get:12 http://incoming.debian.org/debian-buildd buildd-unstable/main kfreebsd-i386 Packages [97.2 kB]
+Get:13 http://incoming.debian.org/debian-buildd buildd-unstable/contrib kfreebsd-i386 Packages [872 B]
+Get:14 http://ftp.debian.org/debian unstable/main kfreebsd-i386 Packages [7099 kB]
+Get:15 http://incoming.debian.org/debian-buildd buildd-experimental/main Sources [30.7 kB]
+Get:16 http://incoming.debian.org/debian-buildd buildd-experimental/main kfreebsd-i386 Packages [46.2 kB]
+Get:17 http://ftp.debian.org/debian unstable/contrib kfreebsd-i386 Packages [42.0 kB]
+Get:18 http://ftp.debian.org/debian experimental/main Sources [262 kB]
+Get:19 http://ftp.debian.org/debian experimental/non-free Sources [3012 B]
+Get:20 http://ftp.debian.org/debian experimental/contrib Sources [1692 B]
+Get:21 http://ftp.debian.org/debian experimental/contrib kfreebsd-i386 Packages [824 B]
+Get:22 http://ftp.debian.org/debian experimental/main kfreebsd-i386 Packages [327 kB]
+Get:23 http://ftp.de.debian.org/debian unstable/main Sources [7953 kB]
+Get:24 http://ftp.de.debian.org/debian unstable/non-free Sources [83.9 kB]
+Get:25 http://ftp.de.debian.org/debian unstable/contrib Sources [50.5 kB]
+Get:26 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 Packages [7099 kB]
+Get:27 http://ftp.de.debian.org/debian unstable/contrib kfreebsd-i386 Packages [42.0 kB]
+Get:28 http://ftp.de.debian.org/debian experimental/contrib Sources [1692 B]
+Get:29 http://ftp.de.debian.org/debian experimental/main Sources [262 kB]
+Get:30 http://ftp.de.debian.org/debian experimental/non-free Sources [3012 B]
+Get:31 http://ftp.de.debian.org/debian experimental/main kfreebsd-i386 Packages [327 kB]
+Get:32 http://ftp.de.debian.org/debian experimental/contrib kfreebsd-i386 Packages [824 B]
+Fetched 32.8 MB in 14s (2316 kB/s)
+Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Fetch source files │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Check APT
+─────────
+
+Checking available source versions...
+W: apt-cache output for different version
+
+Download source files with APT
+──────────────────────────────
+
+Reading package lists...
+NOTICE: 'bcftools' packaging is maintained in the 'Git' version control system at:
+https://anonscm.debian.org/git/debian-med/bcftools.git
+Please use:
+git clone https://anonscm.debian.org/git/debian-med/bcftools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 2342 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (dsc) [2110 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (tar) [2333 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (diff) [6088 B]
+Fetched 2342 kB in 0s (6156 kB/s)
+Download complete and in download only mode
+
+Check architectures
+───────────────────
+
+sh: 1: gcc: not found
+sbuild: warning: couldn't determine gcc system type, falling back to default (native compilation)
+
+Check dependencies
+──────────────────
+
+Merged Build-Depends: build-essential, fakeroot
+Filtered Build-Depends: build-essential, fakeroot
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-N2vwZ9/apt_archive/sbuild-build-depends-core-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ Packages [533 B]
+Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install core build dependencies (aptitude-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following additional packages will be installed:
+ aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+Suggested packages:
+ aptitude-doc-en | aptitude-doc apt-xapian-index debtags tasksel
+ libcwidget-dev xapian-tools
+Recommended packages:
+ libparse-debianchangelog-perl
+The following NEW packages will be installed:
+ aptitude aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded.
+Need to get 5632 kB of archives.
+After this operation, 22.2 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libxapian30 kfreebsd-i386 1.4.5-1 [1312 kB]
+Get:2 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libsqlite3-0 kfreebsd-i386 3.21.0-1 [621 kB]
+Get:3 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 aptitude-common all 0.8.10-1 [1591 kB]
+Get:4 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libboost-system1.62.0 kfreebsd-i386 1.62.0+dfsg-4+b2 [33.3 kB]
+Get:5 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libboost-filesystem1.62.0 kfreebsd-i386 1.62.0+dfsg-4+b2 [68.0 kB]
+Get:6 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libboost-iostreams1.62.0 kfreebsd-i386 1.62.0+dfsg-4+b2 [53.2 kB]
+Get:7 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libsigc++-2.0-0v5 kfreebsd-i386 2.10.0-1 [62.2 kB]
+Get:8 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libcwidget3v5 kfreebsd-i386 0.5.17-6 [330 kB]
+Get:9 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 aptitude kfreebsd-i386 0.8.10-1 [1562 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 5632 kB in 0s (7343 kB/s)
+Selecting previously unselected package libxapian30:kfreebsd-i386.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
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(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11637 files and directories currently installed.)
+Preparing to unpack .../0-libxapian30_1.4.5-1_kfreebsd-i386.deb ...
+Unpacking libxapian30:kfreebsd-i386 (1.4.5-1) ...
+Selecting previously unselected package libsqlite3-0:kfreebsd-i386.
+Preparing to unpack .../1-libsqlite3-0_3.21.0-1_kfreebsd-i386.deb ...
+Unpacking libsqlite3-0:kfreebsd-i386 (3.21.0-1) ...
+Selecting previously unselected package aptitude-common.
+Preparing to unpack .../2-aptitude-common_0.8.10-1_all.deb ...
+Unpacking aptitude-common (0.8.10-1) ...
+Selecting previously unselected package libboost-system1.62.0:kfreebsd-i386.
+Preparing to unpack .../3-libboost-system1.62.0_1.62.0+dfsg-4+b2_kfreebsd-i386.deb ...
+Unpacking libboost-system1.62.0:kfreebsd-i386 (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libboost-filesystem1.62.0:kfreebsd-i386.
+Preparing to unpack .../4-libboost-filesystem1.62.0_1.62.0+dfsg-4+b2_kfreebsd-i386.deb ...
+Unpacking libboost-filesystem1.62.0:kfreebsd-i386 (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libboost-iostreams1.62.0:kfreebsd-i386.
+Preparing to unpack .../5-libboost-iostreams1.62.0_1.62.0+dfsg-4+b2_kfreebsd-i386.deb ...
+Unpacking libboost-iostreams1.62.0:kfreebsd-i386 (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libsigc++-2.0-0v5:kfreebsd-i386.
+Preparing to unpack .../6-libsigc++-2.0-0v5_2.10.0-1_kfreebsd-i386.deb ...
+Unpacking libsigc++-2.0-0v5:kfreebsd-i386 (2.10.0-1) ...
+Selecting previously unselected package libcwidget3v5:kfreebsd-i386.
+Preparing to unpack .../7-libcwidget3v5_0.5.17-6_kfreebsd-i386.deb ...
+Unpacking libcwidget3v5:kfreebsd-i386 (0.5.17-6) ...
+Selecting previously unselected package aptitude.
+Preparing to unpack .../8-aptitude_0.8.10-1_kfreebsd-i386.deb ...
+Unpacking aptitude (0.8.10-1) ...
+Setting up libxapian30:kfreebsd-i386 (1.4.5-1) ...
+Setting up aptitude-common (0.8.10-1) ...
+Setting up libboost-iostreams1.62.0:kfreebsd-i386 (1.62.0+dfsg-4+b2) ...
+Processing triggers for libc-bin (2.25-3) ...
+Setting up libsqlite3-0:kfreebsd-i386 (3.21.0-1) ...
+Setting up libsigc++-2.0-0v5:kfreebsd-i386 (2.10.0-1) ...
+Setting up libboost-system1.62.0:kfreebsd-i386 (1.62.0+dfsg-4+b2) ...
+Setting up libboost-filesystem1.62.0:kfreebsd-i386 (1.62.0+dfsg-4+b2) ...
+Setting up libcwidget3v5:kfreebsd-i386 (0.5.17-6) ...
+Setting up aptitude (0.8.10-1) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode
+Processing triggers for libc-bin (2.25-3) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-core-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-core-dummy
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+0 packages upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/860 B of archives. After unpacking 0 B will be used.
+Writing extended state information...
+Get: 1 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [860 B]
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
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(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11894 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, init, libc-bin, login, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:7.2), g++ (>= 4:7.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, init, libc-bin, login, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:7.2), g++ (>= 4:7.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/«BUILDDIR»/resolver-N2vwZ9/apt_archive/sbuild-build-depends-bcftools-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ Sources [511 B]
+Get:5 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ Packages [956 B]
+Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install bcftools build dependencies (aptitude-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+aptitude is already the newest version (0.8.10-1).
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-bcftools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-bcftools-dummy
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} file{a} gettext{a} gettext-base{a} groff-base{a} init{a} initscripts{a} insserv{a} intltool-debian{a} kbdcontrol{a} libarchive-zip-perl{a} libbz2-dev{a} libcroco3{a} libcurl3-gnutls{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libhts-dev{a} libhts2{a} libicu57{a} libidn2-0{a} libio-pty-perl{a} libldap-2.4-2{a} [...]
+The following packages are RECOMMENDED but will NOT be installed:
+ bzip2-doc ca-certificates curl libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl libsasl2-modules psmisc publicsuffix shared-mime-info wget xdg-user-dirs
+0 packages upgraded, 59 newly installed, 0 to remove and 0 not upgraded.
+Need to get 26.8 MB/26.8 MB of archives. After unpacking 90.5 MB will be used.
+Writing extended state information...
+Get: 1 file:/«BUILDDIR»/resolver-N2vwZ9/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [1068 B]
+Get: 2 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 insserv kfreebsd-i386 1.14.0-5.4+b1 [62.8 kB]
+Get: 3 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 startpar kfreebsd-i386 0.59-4 [21.0 kB]
+Get: 4 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 sysv-rc all 2.88dsf-59.10 [67.6 kB]
+Get: 5 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 initscripts kfreebsd-i386 2.88dsf-59.10 [84.5 kB]
+Get: 6 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 kbdcontrol kfreebsd-i386 10.3~svn296373-2 [76.8 kB]
+Get: 7 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 sysvinit-core kfreebsd-i386 2.88dsf-59.10 [135 kB]
+Get: 8 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 init kfreebsd-i386 1.51 [12.9 kB]
+Get: 9 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 groff-base kfreebsd-i386 1.22.3-9 [1186 kB]
+Get: 10 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libncurses5 kfreebsd-i386 6.0+20171125-1 [101 kB]
+Get: 11 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 bsdmainutils kfreebsd-i386 9.0.14 [188 kB]
+Get: 12 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libpipeline1 kfreebsd-i386 1.5.0-1 [31.0 kB]
+Get: 13 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 man-db kfreebsd-i386 2.7.5-2 [1009 kB]
+Get: 14 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libssl1.1 kfreebsd-i386 1.1.0g-2 [1340 kB]
+Get: 15 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libmagic-mgc kfreebsd-i386 1:5.32-1 [225 kB]
+Get: 16 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libmagic1 kfreebsd-i386 1:5.32-1 [117 kB]
+Get: 17 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 file kfreebsd-i386 1:5.32-1 [64.3 kB]
+Get: 18 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 gettext-base kfreebsd-i386 0.19.8.1-4 [123 kB]
+Get: 19 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libsasl2-modules-db kfreebsd-i386 2.1.27~101-g0780600+dfsg-3 [69.1 kB]
+Get: 20 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libsasl2-2 kfreebsd-i386 2.1.27~101-g0780600+dfsg-3 [108 kB]
+Get: 21 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libldap-common all 2.4.45+dfsg-1 [87.0 kB]
+Get: 22 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libldap-2.4-2 kfreebsd-i386 2.4.45+dfsg-1 [232 kB]
+Get: 23 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libicu57 kfreebsd-i386 57.1-8 [7840 kB]
+Get: 24 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libxml2 kfreebsd-i386 2.9.4+dfsg1-5.1 [734 kB]
+Get: 25 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libsigsegv2 kfreebsd-i386 2.11-1 [29.7 kB]
+Get: 26 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 m4 kfreebsd-i386 1.4.18-1 [204 kB]
+Get: 27 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 autoconf all 2.69-11 [341 kB]
+Get: 28 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 autotools-dev all 20161112.1+nmu1 [74.2 kB]
+Get: 29 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 automake all 1:1.15.1-3 [736 kB]
+Get: 30 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 autopoint all 0.19.8.1-4 [434 kB]
+Get: 31 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libtool all 2.4.6-2 [545 kB]
+Get: 32 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 dh-autoreconf all 15 [16.2 kB]
+Get: 33 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libarchive-zip-perl all 1.59-1 [95.5 kB]
+Get: 34 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
+Get: 35 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get: 36 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 dh-strip-nondeterminism all 0.040-1 [11.8 kB]
+Get: 37 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libglib2.0-0 kfreebsd-i386 2.54.2-1 [2880 kB]
+Get: 38 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libcroco3 kfreebsd-i386 0.6.12-1 [150 kB]
+Get: 39 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libunistring2 kfreebsd-i386 0.9.8-1 [386 kB]
+Get: 40 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 gettext kfreebsd-i386 0.19.8.1-4 [1309 kB]
+Get: 41 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get: 42 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 po-debconf all 1.0.20 [247 kB]
+Get: 43 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 debhelper all 10.10.9 [975 kB]
+Get: 44 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libbz2-dev kfreebsd-i386 1.0.6-8.1 [28.6 kB]
+Get: 45 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libidn2-0 kfreebsd-i386 2.0.2-5 [58.9 kB]
+Get: 46 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libnghttp2-14 kfreebsd-i386 1.19.0-2 [89.4 kB]
+Get: 47 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libpsl5 kfreebsd-i386 0.19.1-4 [45.1 kB]
+Get: 48 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 librtmp1 kfreebsd-i386 2.4+20151223.gitfa8646d.1-1+b1 [64.4 kB]
+Get: 49 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libssh2-1 kfreebsd-i386 1.8.0-1 [145 kB]
+Get: 50 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libcurl3-gnutls kfreebsd-i386 7.56.1-1 [331 kB]
+Get: 51 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libgslcblas0 kfreebsd-i386 2.4+dfsg-6 [97.4 kB]
+Get: 52 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libgsl23 kfreebsd-i386 2.4+dfsg-6 [827 kB]
+Get: 53 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libgsl-dev kfreebsd-i386 2.4+dfsg-6 [1041 kB]
+Get: 54 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libhts2 kfreebsd-i386 1.5-6 [317 kB]
+Get: 55 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 liblzma-dev kfreebsd-i386 5.2.2-1.3 [302 kB]
+Get: 56 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 tabix kfreebsd-i386 1.5-6 [341 kB]
+Get: 57 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libhts-dev kfreebsd-i386 1.5-6 [397 kB]
+Get: 58 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libio-pty-perl kfreebsd-i386 1:1.08-1.1+b4 [34.2 kB]
+Get: 59 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 zlib1g-dev kfreebsd-i386 1:1.2.8.dfsg-5 [204 kB]
+Fetched 26.8 MB in 1s (14.7 MB/s)
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package insserv.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11894 files and directories currently installed.)
+Preparing to unpack .../0-insserv_1.14.0-5.4+b1_kfreebsd-i386.deb ...
+Unpacking insserv (1.14.0-5.4+b1) ...
+Selecting previously unselected package startpar.
+Preparing to unpack .../1-startpar_0.59-4_kfreebsd-i386.deb ...
+Unpacking startpar (0.59-4) ...
+Selecting previously unselected package sysv-rc.
+Preparing to unpack .../2-sysv-rc_2.88dsf-59.10_all.deb ...
+Unpacking sysv-rc (2.88dsf-59.10) ...
+Selecting previously unselected package initscripts.
+Preparing to unpack .../3-initscripts_2.88dsf-59.10_kfreebsd-i386.deb ...
+Unpacking initscripts (2.88dsf-59.10) ...
+Selecting previously unselected package kbdcontrol.
+Preparing to unpack .../4-kbdcontrol_10.3~svn296373-2_kfreebsd-i386.deb ...
+Unpacking kbdcontrol (10.3~svn296373-2) ...
+Selecting previously unselected package sysvinit-core.
+Preparing to unpack .../5-sysvinit-core_2.88dsf-59.10_kfreebsd-i386.deb ...
+Unpacking sysvinit-core (2.88dsf-59.10) ...
+Setting up insserv (1.14.0-5.4+b1) ...
+Setting up startpar (0.59-4) ...
+Setting up sysv-rc (2.88dsf-59.10) ...
+Setting up initscripts (2.88dsf-59.10) ...
+invoke-rc.d: could not determine current runlevel
+invoke-rc.d: policy-rc.d denied execution of start.
+Setting up kbdcontrol (10.3~svn296373-2) ...
+update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
+invoke-rc.d: could not determine current runlevel
+invoke-rc.d: policy-rc.d denied execution of start.
+Setting up sysvinit-core (2.88dsf-59.10) ...
+Not restarting sysvinit
+Selecting previously unselected package init.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
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(Reading database ... 12130 files and directories currently installed.)
+Preparing to unpack .../00-init_1.51_kfreebsd-i386.deb ...
+Unpacking init (1.51) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../01-groff-base_1.22.3-9_kfreebsd-i386.deb ...
+Unpacking groff-base (1.22.3-9) ...
+Selecting previously unselected package libncurses5:kfreebsd-i386.
+Preparing to unpack .../02-libncurses5_6.0+20171125-1_kfreebsd-i386.deb ...
+Unpacking libncurses5:kfreebsd-i386 (6.0+20171125-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../03-bsdmainutils_9.0.14_kfreebsd-i386.deb ...
+Unpacking bsdmainutils (9.0.14) ...
+Selecting previously unselected package libpipeline1:kfreebsd-i386.
+Preparing to unpack .../04-libpipeline1_1.5.0-1_kfreebsd-i386.deb ...
+Unpacking libpipeline1:kfreebsd-i386 (1.5.0-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../05-man-db_2.7.5-2_kfreebsd-i386.deb ...
+Unpacking man-db (2.7.5-2) ...
+Selecting previously unselected package libssl1.1:kfreebsd-i386.
+Preparing to unpack .../06-libssl1.1_1.1.0g-2_kfreebsd-i386.deb ...
+Unpacking libssl1.1:kfreebsd-i386 (1.1.0g-2) ...
+Selecting previously unselected package libmagic-mgc.
+Preparing to unpack .../07-libmagic-mgc_1%3a5.32-1_kfreebsd-i386.deb ...
+Unpacking libmagic-mgc (1:5.32-1) ...
+Selecting previously unselected package libmagic1:kfreebsd-i386.
+Preparing to unpack .../08-libmagic1_1%3a5.32-1_kfreebsd-i386.deb ...
+Unpacking libmagic1:kfreebsd-i386 (1:5.32-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../09-file_1%3a5.32-1_kfreebsd-i386.deb ...
+Unpacking file (1:5.32-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../10-gettext-base_0.19.8.1-4_kfreebsd-i386.deb ...
+Unpacking gettext-base (0.19.8.1-4) ...
+Selecting previously unselected package libsasl2-modules-db:kfreebsd-i386.
+Preparing to unpack .../11-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3_kfreebsd-i386.deb ...
+Unpacking libsasl2-modules-db:kfreebsd-i386 (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libsasl2-2:kfreebsd-i386.
+Preparing to unpack .../12-libsasl2-2_2.1.27~101-g0780600+dfsg-3_kfreebsd-i386.deb ...
+Unpacking libsasl2-2:kfreebsd-i386 (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libldap-common.
+Preparing to unpack .../13-libldap-common_2.4.45+dfsg-1_all.deb ...
+Unpacking libldap-common (2.4.45+dfsg-1) ...
+Selecting previously unselected package libldap-2.4-2:kfreebsd-i386.
+Preparing to unpack .../14-libldap-2.4-2_2.4.45+dfsg-1_kfreebsd-i386.deb ...
+Unpacking libldap-2.4-2:kfreebsd-i386 (2.4.45+dfsg-1) ...
+Selecting previously unselected package libicu57:kfreebsd-i386.
+Preparing to unpack .../15-libicu57_57.1-8_kfreebsd-i386.deb ...
+Unpacking libicu57:kfreebsd-i386 (57.1-8) ...
+Selecting previously unselected package libxml2:kfreebsd-i386.
+Preparing to unpack .../16-libxml2_2.9.4+dfsg1-5.1_kfreebsd-i386.deb ...
+Unpacking libxml2:kfreebsd-i386 (2.9.4+dfsg1-5.1) ...
+Selecting previously unselected package libsigsegv2:kfreebsd-i386.
+Preparing to unpack .../17-libsigsegv2_2.11-1_kfreebsd-i386.deb ...
+Unpacking libsigsegv2:kfreebsd-i386 (2.11-1) ...
+Selecting previously unselected package m4.
+Preparing to unpack .../18-m4_1.4.18-1_kfreebsd-i386.deb ...
+Unpacking m4 (1.4.18-1) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../19-autoconf_2.69-11_all.deb ...
+Unpacking autoconf (2.69-11) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../20-autotools-dev_20161112.1+nmu1_all.deb ...
+Unpacking autotools-dev (20161112.1+nmu1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../21-automake_1%3a1.15.1-3_all.deb ...
+Unpacking automake (1:1.15.1-3) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../22-autopoint_0.19.8.1-4_all.deb ...
+Unpacking autopoint (0.19.8.1-4) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../23-libtool_2.4.6-2_all.deb ...
+Unpacking libtool (2.4.6-2) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../24-dh-autoreconf_15_all.deb ...
+Unpacking dh-autoreconf (15) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../25-libarchive-zip-perl_1.59-1_all.deb ...
+Unpacking libarchive-zip-perl (1.59-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../26-libfile-stripnondeterminism-perl_0.040-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.040-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../27-libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../28-dh-strip-nondeterminism_0.040-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.040-1) ...
+Selecting previously unselected package libglib2.0-0:kfreebsd-i386.
+Preparing to unpack .../29-libglib2.0-0_2.54.2-1_kfreebsd-i386.deb ...
+Unpacking libglib2.0-0:kfreebsd-i386 (2.54.2-1) ...
+Selecting previously unselected package libcroco3:kfreebsd-i386.
+Preparing to unpack .../30-libcroco3_0.6.12-1_kfreebsd-i386.deb ...
+Unpacking libcroco3:kfreebsd-i386 (0.6.12-1) ...
+Selecting previously unselected package libunistring2:kfreebsd-i386.
+Preparing to unpack .../31-libunistring2_0.9.8-1_kfreebsd-i386.deb ...
+Unpacking libunistring2:kfreebsd-i386 (0.9.8-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../32-gettext_0.19.8.1-4_kfreebsd-i386.deb ...
+Unpacking gettext (0.19.8.1-4) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../33-intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../34-po-debconf_1.0.20_all.deb ...
+Unpacking po-debconf (1.0.20) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../35-debhelper_10.10.9_all.deb ...
+Unpacking debhelper (10.10.9) ...
+Selecting previously unselected package libbz2-dev:kfreebsd-i386.
+Preparing to unpack .../36-libbz2-dev_1.0.6-8.1_kfreebsd-i386.deb ...
+Unpacking libbz2-dev:kfreebsd-i386 (1.0.6-8.1) ...
+Selecting previously unselected package libidn2-0:kfreebsd-i386.
+Preparing to unpack .../37-libidn2-0_2.0.2-5_kfreebsd-i386.deb ...
+Unpacking libidn2-0:kfreebsd-i386 (2.0.2-5) ...
+Selecting previously unselected package libnghttp2-14:kfreebsd-i386.
+Preparing to unpack .../38-libnghttp2-14_1.19.0-2_kfreebsd-i386.deb ...
+Unpacking libnghttp2-14:kfreebsd-i386 (1.19.0-2) ...
+Selecting previously unselected package libpsl5:kfreebsd-i386.
+Preparing to unpack .../39-libpsl5_0.19.1-4_kfreebsd-i386.deb ...
+Unpacking libpsl5:kfreebsd-i386 (0.19.1-4) ...
+Selecting previously unselected package librtmp1:kfreebsd-i386.
+Preparing to unpack .../40-librtmp1_2.4+20151223.gitfa8646d.1-1+b1_kfreebsd-i386.deb ...
+Unpacking librtmp1:kfreebsd-i386 (2.4+20151223.gitfa8646d.1-1+b1) ...
+Selecting previously unselected package libssh2-1:kfreebsd-i386.
+Preparing to unpack .../41-libssh2-1_1.8.0-1_kfreebsd-i386.deb ...
+Unpacking libssh2-1:kfreebsd-i386 (1.8.0-1) ...
+Selecting previously unselected package libcurl3-gnutls:kfreebsd-i386.
+Preparing to unpack .../42-libcurl3-gnutls_7.56.1-1_kfreebsd-i386.deb ...
+Unpacking libcurl3-gnutls:kfreebsd-i386 (7.56.1-1) ...
+Selecting previously unselected package libgslcblas0:kfreebsd-i386.
+Preparing to unpack .../43-libgslcblas0_2.4+dfsg-6_kfreebsd-i386.deb ...
+Unpacking libgslcblas0:kfreebsd-i386 (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl23:kfreebsd-i386.
+Preparing to unpack .../44-libgsl23_2.4+dfsg-6_kfreebsd-i386.deb ...
+Unpacking libgsl23:kfreebsd-i386 (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl-dev.
+Preparing to unpack .../45-libgsl-dev_2.4+dfsg-6_kfreebsd-i386.deb ...
+Unpacking libgsl-dev (2.4+dfsg-6) ...
+Selecting previously unselected package libhts2:kfreebsd-i386.
+Preparing to unpack .../46-libhts2_1.5-6_kfreebsd-i386.deb ...
+Unpacking libhts2:kfreebsd-i386 (1.5-6) ...
+Selecting previously unselected package liblzma-dev:kfreebsd-i386.
+Preparing to unpack .../47-liblzma-dev_5.2.2-1.3_kfreebsd-i386.deb ...
+Unpacking liblzma-dev:kfreebsd-i386 (5.2.2-1.3) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../48-tabix_1.5-6_kfreebsd-i386.deb ...
+Unpacking tabix (1.5-6) ...
+Selecting previously unselected package libhts-dev:kfreebsd-i386.
+Preparing to unpack .../49-libhts-dev_1.5-6_kfreebsd-i386.deb ...
+Unpacking libhts-dev:kfreebsd-i386 (1.5-6) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../50-libio-pty-perl_1%3a1.08-1.1+b4_kfreebsd-i386.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b4) ...
+Selecting previously unselected package zlib1g-dev:kfreebsd-i386.
+Preparing to unpack .../51-zlib1g-dev_1%3a1.2.8.dfsg-5_kfreebsd-i386.deb ...
+Unpacking zlib1g-dev:kfreebsd-i386 (1:1.2.8.dfsg-5) ...
+Selecting previously unselected package sbuild-build-depends-bcftools-dummy.
+Preparing to unpack .../52-sbuild-build-depends-bcftools-dummy.deb ...
+Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Setting up libncurses5:kfreebsd-i386 (6.0+20171125-1) ...
+Setting up libunistring2:kfreebsd-i386 (0.9.8-1) ...
+Setting up libbz2-dev:kfreebsd-i386 (1.0.6-8.1) ...
+Setting up libidn2-0:kfreebsd-i386 (2.0.2-5) ...
+Setting up libarchive-zip-perl (1.59-1) ...
+Setting up libnghttp2-14:kfreebsd-i386 (1.19.0-2) ...
+Setting up libio-pty-perl (1:1.08-1.1+b4) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libsigsegv2:kfreebsd-i386 (2.11-1) ...
+Setting up libldap-common (2.4.45+dfsg-1) ...
+Setting up libpsl5:kfreebsd-i386 (0.19.1-4) ...
+Setting up init (1.51) ...
+Setting up groff-base (1.22.3-9) ...
+Setting up libglib2.0-0:kfreebsd-i386 (2.54.2-1) ...
+No schema files found: doing nothing.
+Setting up libsasl2-modules-db:kfreebsd-i386 (2.1.27~101-g0780600+dfsg-3) ...
+Setting up libsasl2-2:kfreebsd-i386 (2.1.27~101-g0780600+dfsg-3) ...
+Setting up gettext-base (0.19.8.1-4) ...
+Setting up libpipeline1:kfreebsd-i386 (1.5.0-1) ...
+Setting up librtmp1:kfreebsd-i386 (2.4+20151223.gitfa8646d.1-1+b1) ...
+Setting up m4 (1.4.18-1) ...
+Setting up libicu57:kfreebsd-i386 (57.1-8) ...
+Setting up libxml2:kfreebsd-i386 (2.9.4+dfsg1-5.1) ...
+Setting up libmagic-mgc (1:5.32-1) ...
+Setting up libmagic1:kfreebsd-i386 (1:5.32-1) ...
+Setting up libcroco3:kfreebsd-i386 (0.6.12-1) ...
+Setting up libssh2-1:kfreebsd-i386 (1.8.0-1) ...
+Processing triggers for libc-bin (2.25-3) ...
+Setting up autotools-dev (20161112.1+nmu1) ...
+Setting up libldap-2.4-2:kfreebsd-i386 (2.4.45+dfsg-1) ...
+Setting up libssl1.1:kfreebsd-i386 (1.1.0g-2) ...
+Setting up liblzma-dev:kfreebsd-i386 (5.2.2-1.3) ...
+Setting up bsdmainutils (9.0.14) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libgslcblas0:kfreebsd-i386 (2.4+dfsg-6) ...
+Setting up autopoint (0.19.8.1-4) ...
+Setting up zlib1g-dev:kfreebsd-i386 (1:1.2.8.dfsg-5) ...
+Setting up libfile-stripnondeterminism-perl (0.040-1) ...
+Setting up libgsl23:kfreebsd-i386 (2.4+dfsg-6) ...
+Setting up gettext (0.19.8.1-4) ...
+Setting up libgsl-dev (2.4+dfsg-6) ...
+Setting up libcurl3-gnutls:kfreebsd-i386 (7.56.1-1) ...
+Setting up autoconf (2.69-11) ...
+Setting up file (1:5.32-1) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up automake (1:1.15.1-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
+Setting up man-db (2.7.5-2) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up tabix (1.5-6) ...
+Setting up libhts2:kfreebsd-i386 (1.5-6) ...
+Setting up libtool (2.4.6-2) ...
+Setting up po-debconf (1.0.20) ...
+Setting up libhts-dev:kfreebsd-i386 (1.5-6) ...
+Setting up dh-autoreconf (15) ...
+Setting up dh-strip-nondeterminism (0.040-1) ...
+Setting up debhelper (10.10.9) ...
+Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.25-3) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Kernel: GNU/kFreeBSD 10.1-0-686 kfreebsd-i386 (i386)
+Toolchain package versions: binutils_2.29.1-11 dpkg-dev_1.19.0.4 g++-7_7.2.0-17 gcc-7_7.2.0-17 kfreebsd-kernel-headers_10.3~6 libc0.1-dev_2.25-3 libstdc++-7-dev_7.2.0-17 libstdc++6_7.2.0-17
+Package versions: adduser_3.116 apt_1.6~alpha5 aptitude_0.8.10-1 aptitude-common_0.8.10-1 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-11 binutils-common_2.29.1-11 binutils-i686-kfreebsd-gnu_2.29.1-11 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 coreutils_8.28-1 cpp_4:7.2.0-1d1 cpp-7_7.2.0-17 dash_0.5.8-2.5 debconf_1.5.65 debhelper_10.10.9 debian-archiv [...]
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Unpack source
+─────────────
+
+gpgv: unknown type of key resource 'trustedkeys.kbx'
+gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
+gpgv: Signature made Mon Dec 11 14:53:09 2017 UTC
+gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
+gpgv: issuer "tillea at rki.de"
+gpgv: Can't check signature: No public key
+dpkg-source: warning: failed to verify signature on ./bcftools_1.6-1.dsc
+dpkg-source: info: extracting bcftools in bcftools-1.6
+dpkg-source: info: unpacking bcftools_1.6.orig.tar.gz
+dpkg-source: info: unpacking bcftools_1.6-1.debian.tar.xz
+dpkg-source: info: applying tests-pluginpath.patch
+dpkg-source: info: applying test-regidx-unsigned-char.patch
+dpkg-source: info: applying fix-test_vcf_query.patch
+
+Check disc space
+────────────────
+
+Sufficient free space for build
+
+User Environment
+────────────────
+
+DEB_BUILD_OPTIONS=parallel=2
+HOME=/sbuild-nonexistent
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=experimental-kfreebsd-i386-sbuild
+SCHROOT_CHROOT_NAME=experimental-k-i-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1009
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=experimental-k-i-sbuild-1513009279-42128
+SCHROOT_UID=2952
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
+
+dpkg-buildpackage
+─────────────────
+
+dpkg-buildpackage: info: source package bcftools
+dpkg-buildpackage: info: source version 1.6-1
+dpkg-buildpackage: info: source distribution experimental
+ dpkg-source --before-build bcftools-1.6
+dpkg-buildpackage: info: host architecture kfreebsd-i386
+ fakeroot debian/rules clean
+rm -f config.mk && touch config.mk
+dh clean --parallel
+ dh_auto_clean
+ make -j2 distclean
+make[1]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.o test/*~
+rm -f plugins/*.so plugins/*.P
+rm -rf plugins/*.dSYM
+rm -f gmon.out *.o *~ version.h plugins/*.so plugins/*.P
+rm -rf *.dSYM plugins/*.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 '/«PKGBUILDDIR»'
+ dh_clean
+ debian/rules build-arch
+dh build-arch --parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_autoreconf
+make[1]: Entering directory '/«PKGBUILDDIR»'
+rm -f config.mk && touch config.mk
+export MAKEFLAGS="-s"; dh_autoreconf
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_configure -- \
+--with-htslib=system \
+--enable-gsl \
+--with-cblas=gslcblas \
+--with-bcf-plugin-dir=/usr/lib/i386-kfreebsd-gnu/bcftools
+ ./configure --build=i686-kfreebsd-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-kfreebsd-gnu --libexecdir=\${prefix}/lib/i386-kfreebsd-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/i386-kfreebsd-gnu/bcftools
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... no
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking shared library type... plain .so
+checking for library containing dlopen... -ldl
+checking if the compiler accepts -rdynamic... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_auto_build -a -O--parallel
+ make -j2
+make[1]: Entering directory '/«PKGBUILDDIR»'
+echo '#define BCFTOOLS_VERSION "1.6"' > version.h
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/i386-kfreebsd-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -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 -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -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 -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl
+gcc -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c
+gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl
+gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -ldl -ldl
+gcc -rdynamic -pthread -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 vcfplugin.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 ccall.o em.o prob1.o kmin.o -l [...]
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_auto_test -a -O--parallel
+ make -j2 test VERBOSE=1
+make[1]: Entering directory '/«PKGBUILDDIR»'
+./test/test-rbuf
+Inserted 1-9 starting at offset 5:
+ 5 6 7 8 9 0 1 2 3
+ 1 2 3 4 5 6 7 8 9
+4th is 4
+Deleting 1-2:
+ 7 8 9 0 1 2 3
+ 3 4 5 6 7 8 9
+Prepending 0-8:
+ 8 9 0 1 2 3 4 5 6 7
+ 8 7 6 5 4 3 2 1 0 3
+Expanding:
+ 8 9 10 11 12 13 14 15 16 17
+ 8 7 6 5 4 3 2 1 0 3
+./test/test-regidx
+REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix=
+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/hB2vxVgGqd/merge.a.vcf.gz 2:3199812-3199812
+.. ok
+
+test_tabix:
+ /«PKGBUILDDIR»/bcftools view -H /tmp/hB2vxVgGqd/merge.a.bcf 2:3199812-3199812
+.. ok
+
+test_tabix:
+ tabix /tmp/hB2vxVgGqd/merge.a.vcf.gz 1:3000151-3000151
+.. ok
+
+test_tabix:
+ /«PKGBUILDDIR»/bcftools view -H /tmp/hB2vxVgGqd/merge.a.bcf 1:3000151-3000151
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/bcftools view -H /tmp/hB2vxVgGqd/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/bcftools view -H /tmp/hB2vxVgGqd/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/bcftools view -H /tmp/hB2vxVgGqd/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/bcftools view -H /tmp/hB2vxVgGqd/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/bcftools view -H /tmp/hB2vxVgGqd/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/bcftools view -H /tmp/hB2vxVgGqd/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/bcftools view -H /tmp/hB2vxVgGqd/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/bcftools view -H /tmp/hB2vxVgGqd/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/bcftools view -H /tmp/hB2vxVgGqd/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/bcftools view -H /tmp/hB2vxVgGqd/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_vcf_idxstats:
+ /«PKGBUILDDIR»/bcftools index -s /tmp/hB2vxVgGqd/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /«PKGBUILDDIR»/bcftools index -s /tmp/hB2vxVgGqd/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /«PKGBUILDDIR»/bcftools index -s /tmp/hB2vxVgGqd/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /«PKGBUILDDIR»/bcftools index -n /tmp/hB2vxVgGqd/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /«PKGBUILDDIR»/bcftools index -n /tmp/hB2vxVgGqd/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /«PKGBUILDDIR»/bcftools index -n /tmp/hB2vxVgGqd/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /«PKGBUILDDIR»/bcftools index -s /tmp/hB2vxVgGqd/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /«PKGBUILDDIR»/bcftools index -s /tmp/hB2vxVgGqd/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /«PKGBUILDDIR»/bcftools index -s /tmp/hB2vxVgGqd/empty.bcf
+.. ok
+
+test_vcf_idxstats:
+ /«PKGBUILDDIR»/bcftools index -n /tmp/hB2vxVgGqd/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /«PKGBUILDDIR»/bcftools index -n /tmp/hB2vxVgGqd/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /«PKGBUILDDIR»/bcftools index -n /tmp/hB2vxVgGqd/empty.bcf
+.. ok
+
+test_vcf_check:
+ /«PKGBUILDDIR»/bcftools stats -s - /tmp/hB2vxVgGqd/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/check.vcf.gz | /«PKGBUILDDIR»/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check_merge:
+ /«PKGBUILDDIR»/misc/plot-vcfstats -m /tmp/hB2vxVgGqd/check.1.chk /tmp/hB2vxVgGqd/check.2.chk /tmp/hB2vxVgGqd/check.3.chk /tmp/hB2vxVgGqd/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /«PKGBUILDDIR»/bcftools stats -s - /tmp/hB2vxVgGqd/stats.a.vcf.gz /tmp/hB2vxVgGqd/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /«PKGBUILDDIR»/bcftools stats -s B /tmp/hB2vxVgGqd/stats.a.vcf.gz /tmp/hB2vxVgGqd/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /«PKGBUILDDIR»/bcftools stats -s - /tmp/hB2vxVgGqd/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_isec:
+ /«PKGBUILDDIR»/bcftools isec -n =2 /tmp/hB2vxVgGqd/isec.a.vcf.gz /tmp/hB2vxVgGqd/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /«PKGBUILDDIR»/bcftools isec -Ob -n =2 /tmp/hB2vxVgGqd/isec.a.vcf.gz /tmp/hB2vxVgGqd/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /«PKGBUILDDIR»/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/hB2vxVgGqd/isec.a.vcf.gz /tmp/hB2vxVgGqd/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /«PKGBUILDDIR»/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/hB2vxVgGqd/isec.a.vcf.gz /tmp/hB2vxVgGqd/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /«PKGBUILDDIR»/bcftools isec -n =2 -c both /tmp/hB2vxVgGqd/isec.a.vcf.gz /tmp/hB2vxVgGqd/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /«PKGBUILDDIR»/bcftools isec -Ob -n =2 -c both /tmp/hB2vxVgGqd/isec.a.vcf.gz /tmp/hB2vxVgGqd/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /«PKGBUILDDIR»/bcftools isec -n =2 -c any /tmp/hB2vxVgGqd/isec.a.vcf.gz /tmp/hB2vxVgGqd/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /«PKGBUILDDIR»/bcftools isec -Ob -n =2 -c any /tmp/hB2vxVgGqd/isec.a.vcf.gz /tmp/hB2vxVgGqd/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /«PKGBUILDDIR»/bcftools isec -C -c any /tmp/hB2vxVgGqd/isec.a.vcf.gz /tmp/hB2vxVgGqd/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /«PKGBUILDDIR»/bcftools isec -Ob -C -c any /tmp/hB2vxVgGqd/isec.a.vcf.gz /tmp/hB2vxVgGqd/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec2:
+ /«PKGBUILDDIR»/bcftools isec --no-version -T /tmp/hB2vxVgGqd/isec.tab.gz /tmp/hB2vxVgGqd/isec.a.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec2:
+ /«PKGBUILDDIR»/bcftools isec -Ob -T /tmp/hB2vxVgGqd/isec.tab.gz /tmp/hB2vxVgGqd/isec.a.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge --no-version --force-samples /tmp/hB2vxVgGqd/merge.a.vcf.gz /tmp/hB2vxVgGqd/merge.b.vcf.gz /tmp/hB2vxVgGqd/merge.c.vcf.gz
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.abc.out
+ /«PKGBUILDDIR»/test/merge.abc.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge -Ob --force-samples /tmp/hB2vxVgGqd/merge.a.vcf.gz /tmp/hB2vxVgGqd/merge.b.vcf.gz /tmp/hB2vxVgGqd/merge.c.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.abc.out
+ /«PKGBUILDDIR»/test/merge.abc.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge --no-version --force-samples -Fx /tmp/hB2vxVgGqd/merge.a.vcf.gz /tmp/hB2vxVgGqd/merge.b.vcf.gz /tmp/hB2vxVgGqd/merge.c.vcf.gz
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.abc.2.out
+ /«PKGBUILDDIR»/test/merge.abc.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge -Ob --force-samples -Fx /tmp/hB2vxVgGqd/merge.a.vcf.gz /tmp/hB2vxVgGqd/merge.b.vcf.gz /tmp/hB2vxVgGqd/merge.c.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.abc.2.out
+ /«PKGBUILDDIR»/test/merge.abc.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge --no-version --force-samples -0 /tmp/hB2vxVgGqd/merge.a.vcf.gz /tmp/hB2vxVgGqd/merge.b.vcf.gz /tmp/hB2vxVgGqd/merge.c.vcf.gz
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.abc.3.out
+ /«PKGBUILDDIR»/test/merge.abc.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge -Ob --force-samples -0 /tmp/hB2vxVgGqd/merge.a.vcf.gz /tmp/hB2vxVgGqd/merge.b.vcf.gz /tmp/hB2vxVgGqd/merge.c.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.abc.3.out
+ /«PKGBUILDDIR»/test/merge.abc.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge --no-version --force-samples -m none /tmp/hB2vxVgGqd/merge.2.a.vcf.gz /tmp/hB2vxVgGqd/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.2.none.out
+ /«PKGBUILDDIR»/test/merge.2.none.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge -Ob --force-samples -m none /tmp/hB2vxVgGqd/merge.2.a.vcf.gz /tmp/hB2vxVgGqd/merge.2.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.2.none.out
+ /«PKGBUILDDIR»/test/merge.2.none.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge --no-version --force-samples -m both /tmp/hB2vxVgGqd/merge.2.a.vcf.gz /tmp/hB2vxVgGqd/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.2.both.out
+ /«PKGBUILDDIR»/test/merge.2.both.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge -Ob --force-samples -m both /tmp/hB2vxVgGqd/merge.2.a.vcf.gz /tmp/hB2vxVgGqd/merge.2.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.2.both.out
+ /«PKGBUILDDIR»/test/merge.2.both.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge --no-version --force-samples -m all /tmp/hB2vxVgGqd/merge.2.a.vcf.gz /tmp/hB2vxVgGqd/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.2.all.out
+ /«PKGBUILDDIR»/test/merge.2.all.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge -Ob --force-samples -m all /tmp/hB2vxVgGqd/merge.2.a.vcf.gz /tmp/hB2vxVgGqd/merge.2.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.2.all.out
+ /«PKGBUILDDIR»/test/merge.2.all.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/hB2vxVgGqd/merge.3.a.vcf.gz /tmp/hB2vxVgGqd/merge.3.b.vcf.gz
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.3.out
+ /«PKGBUILDDIR»/test/merge.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/hB2vxVgGqd/merge.3.a.vcf.gz /tmp/hB2vxVgGqd/merge.3.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.3.out
+ /«PKGBUILDDIR»/test/merge.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge --no-version --force-samples -m id /tmp/hB2vxVgGqd/merge.4.a.vcf.gz /tmp/hB2vxVgGqd/merge.4.b.vcf.gz
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.4.out
+ /«PKGBUILDDIR»/test/merge.4.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge -Ob --force-samples -m id /tmp/hB2vxVgGqd/merge.4.a.vcf.gz /tmp/hB2vxVgGqd/merge.4.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.4.out
+ /«PKGBUILDDIR»/test/merge.4.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge --no-version --gvcf - /tmp/hB2vxVgGqd/gvcf.merge.1.vcf.gz /tmp/hB2vxVgGqd/gvcf.merge.2.vcf.gz /tmp/hB2vxVgGqd/gvcf.merge.3.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge -Ob --gvcf - /tmp/hB2vxVgGqd/gvcf.merge.1.vcf.gz /tmp/hB2vxVgGqd/gvcf.merge.2.vcf.gz /tmp/hB2vxVgGqd/gvcf.merge.3.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge --no-version --gvcf - /tmp/hB2vxVgGqd/merge.gvcf.2.a.vcf.gz /tmp/hB2vxVgGqd/merge.gvcf.2.b.vcf.gz /tmp/hB2vxVgGqd/merge.gvcf.2.c.vcf.gz
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.gvcf.2.out
+ /«PKGBUILDDIR»/test/merge.gvcf.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge -Ob --gvcf - /tmp/hB2vxVgGqd/merge.gvcf.2.a.vcf.gz /tmp/hB2vxVgGqd/merge.gvcf.2.b.vcf.gz /tmp/hB2vxVgGqd/merge.gvcf.2.c.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/merge.gvcf.2.out
+ /«PKGBUILDDIR»/test/merge.gvcf.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge --no-version --gvcf - -i SRC:join /tmp/hB2vxVgGqd/merge.gvcf.3.a.vcf.gz /tmp/hB2vxVgGqd/merge.gvcf.3.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge -Ob --gvcf - -i SRC:join /tmp/hB2vxVgGqd/merge.gvcf.3.a.vcf.gz /tmp/hB2vxVgGqd/merge.gvcf.3.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge --no-version /tmp/hB2vxVgGqd/merge.5.a.vcf.gz /tmp/hB2vxVgGqd/merge.5.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /«PKGBUILDDIR»/bcftools merge -Ob /tmp/hB2vxVgGqd/merge.5.a.vcf.gz /tmp/hB2vxVgGqd/merge.5.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/hB2vxVgGqd/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XRI\n' -i'XRI[*]>1111'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XRF\n' -i'XRF[*]=2e6'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[2]~"H"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[*]~"H"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' /tmp/hB2vxVgGqd/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/hB2vxVgGqd/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/hB2vxVgGqd/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10' /tmp/hB2vxVgGqd/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/hB2vxVgGqd/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/hB2vxVgGqd/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/hB2vxVgGqd/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/hB2vxVgGqd/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/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/hB2vxVgGqd/view.vectors.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.vectors.vcf.gz | /«PKGBUILDDIR»/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:
+ /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' /tmp/hB2vxVgGqd/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' /tmp/hB2vxVgGqd/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' /tmp/hB2vxVgGqd/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' /tmp/hB2vxVgGqd/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/hB2vxVgGqd/query.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.2.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -i'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -i'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -e'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -e'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -i'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -e'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -i'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -e'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%LINE' /tmp/hB2vxVgGqd/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%LINE'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/hB2vxVgGqd/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.filter-type.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/hB2vxVgGqd/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.filter-type.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/hB2vxVgGqd/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.filter-type.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/hB2vxVgGqd/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.filter-type.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/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/hB2vxVgGqd/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/filter-missing-floats.vcf.gz | /«PKGBUILDDIR»/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:
+ /«PKGBUILDDIR»/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/hB2vxVgGqd/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/filter-missing-floats.vcf.gz | /«PKGBUILDDIR»/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:
+ /«PKGBUILDDIR»/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/hB2vxVgGqd/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/missing.vcf.gz | /«PKGBUILDDIR»/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/hB2vxVgGqd/query.filter.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/query.filter.2.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6'
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5'
+.. ok
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm --no-version -cx -f /«PKGBUILDDIR»/test/norm.fa /tmp/hB2vxVgGqd/norm.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm -Ob -cx -f /«PKGBUILDDIR»/test/norm.fa /tmp/hB2vxVgGqd/norm.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm --no-version -m- /tmp/hB2vxVgGqd/norm.split.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/norm.split.out
+ /«PKGBUILDDIR»/test/norm.split.out.new
+.. failed ...
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm -Ob -m- /tmp/hB2vxVgGqd/norm.split.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/norm.split.out
+ /«PKGBUILDDIR»/test/norm.split.out.new
+.. failed ...
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm --no-version -m- /tmp/hB2vxVgGqd/norm.split.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm -Ob -m- /tmp/hB2vxVgGqd/norm.split.2.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm --no-version -m- -f /«PKGBUILDDIR»/test/norm.fa /tmp/hB2vxVgGqd/norm.split.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/norm.split.and.norm.out
+ /«PKGBUILDDIR»/test/norm.split.and.norm.out.new
+.. failed ...
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm -Ob -m- -f /«PKGBUILDDIR»/test/norm.fa /tmp/hB2vxVgGqd/norm.split.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/norm.split.and.norm.out
+ /«PKGBUILDDIR»/test/norm.split.and.norm.out.new
+.. failed ...
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm --no-version -m+ /tmp/hB2vxVgGqd/norm.merge.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/norm.merge.out
+ /«PKGBUILDDIR»/test/norm.merge.out.new
+.. failed ...
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm -Ob -m+ /tmp/hB2vxVgGqd/norm.merge.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/norm.merge.out
+ /«PKGBUILDDIR»/test/norm.merge.out.new
+.. failed ...
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm --no-version -m+ /tmp/hB2vxVgGqd/norm.merge.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm -Ob -m+ /tmp/hB2vxVgGqd/norm.merge.2.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm --no-version -m+ /tmp/hB2vxVgGqd/norm.merge.3.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/norm.merge.3.out
+ /«PKGBUILDDIR»/test/norm.merge.3.out.new
+.. failed ...
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm -Ob -m+ /tmp/hB2vxVgGqd/norm.merge.3.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+[W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.'
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/norm.merge.3.out
+ /«PKGBUILDDIR»/test/norm.merge.3.out.new
+.. failed ...
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm --no-version -m+ -s /tmp/hB2vxVgGqd/norm.merge.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/norm.merge.strict.out
+ /«PKGBUILDDIR»/test/norm.merge.strict.out.new
+.. failed ...
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm -Ob -m+ -s /tmp/hB2vxVgGqd/norm.merge.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/norm.merge.strict.out
+ /«PKGBUILDDIR»/test/norm.merge.strict.out.new
+.. failed ...
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm --no-version -Nc s -f /«PKGBUILDDIR»/test/norm.fa /tmp/hB2vxVgGqd/norm.setref.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm -Ob -Nc s -f /«PKGBUILDDIR»/test/norm.fa /tmp/hB2vxVgGqd/norm.setref.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm --no-version -f /«PKGBUILDDIR»/test/norm.fa /tmp/hB2vxVgGqd/norm.telomere.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /«PKGBUILDDIR»/bcftools norm -Ob -f /«PKGBUILDDIR»/test/norm.fa /tmp/hB2vxVgGqd/norm.telomere.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/hB2vxVgGqd/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/hB2vxVgGqd/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -f PASS -Xks NA00003 /tmp/hB2vxVgGqd/view.vcf.gz -r20,Y
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -f PASS -Xks NA00003 /tmp/hB2vxVgGqd/view.vcf.gz -r20,Y | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -xs NA00003 /tmp/hB2vxVgGqd/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -xs NA00003 /tmp/hB2vxVgGqd/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/hB2vxVgGqd/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/hB2vxVgGqd/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -p /tmp/hB2vxVgGqd/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -p /tmp/hB2vxVgGqd/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -P /tmp/hB2vxVgGqd/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -P /tmp/hB2vxVgGqd/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/hB2vxVgGqd/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/hB2vxVgGqd/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -Hu /tmp/hB2vxVgGqd/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -GVsnps /tmp/hB2vxVgGqd/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -GVsnps /tmp/hB2vxVgGqd/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/hB2vxVgGqd/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/hB2vxVgGqd/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -s ^NA00003 /tmp/hB2vxVgGqd/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -s ^NA00003 /tmp/hB2vxVgGqd/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version /tmp/hB2vxVgGqd/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/view.omitgenotypes.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -G /tmp/hB2vxVgGqd/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -G /tmp/hB2vxVgGqd/view.omitgenotypes.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -HG /tmp/hB2vxVgGqd/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -a /tmp/hB2vxVgGqd/many.alleles.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -a /tmp/hB2vxVgGqd/many.alleles.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -asA /tmp/hB2vxVgGqd/view.vectors.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -asA /tmp/hB2vxVgGqd/view.vectors.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -asB /tmp/hB2vxVgGqd/view.vectors.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -asB /tmp/hB2vxVgGqd/view.vectors.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -asA /tmp/hB2vxVgGqd/view.vectors.2.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -asA /tmp/hB2vxVgGqd/view.vectors.2.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -H -i'FMT/FGS[0]="AAAAAA"' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -H -i'FMT/FGS[2]="C"' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -H -i'FMT/FGS[4]="EE"' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -H -i'FMT/FRS[1]="BB"' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -H -i'TXT0="text"' /tmp/hB2vxVgGqd/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -T /«PKGBUILDDIR»/test/view.chrs.tab /tmp/hB2vxVgGqd/view.chrs.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -T /«PKGBUILDDIR»/test/view.chrs.tab /tmp/hB2vxVgGqd/view.chrs.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -i 'POS>=3062917' /tmp/hB2vxVgGqd/filter.2.vcf.gz 1:3062917-3157410
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view -Ob -i 'POS>=3062917' /tmp/hB2vxVgGqd/filter.2.vcf.gz 1:3062917-3157410 | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -S. -e'TXT0="text"' /«PKGBUILDDIR»/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -S. -e'TXT0="text"' /«PKGBUILDDIR»/test/view.filter.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -S. -e'FMT/FRS[1]="BB"' /«PKGBUILDDIR»/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -S. -e'FMT/FRS[1]="BB"' /«PKGBUILDDIR»/test/view.filter.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -S. -e'FMT/FGS[0]="AAAAAA"' /«PKGBUILDDIR»/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -S. -e'FMT/FGS[0]="AAAAAA"' /«PKGBUILDDIR»/test/view.filter.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -S. -e'FMT/FGS[1]="BBB"' /«PKGBUILDDIR»/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -S. -e'FMT/FGS[1]="BBB"' /«PKGBUILDDIR»/test/view.filter.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -S. -e'FMT/FGS[4]="EE"' /«PKGBUILDDIR»/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -S. -e'FMT/FGS[4]="EE"' /«PKGBUILDDIR»/test/view.filter.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -S. -e'FMT/STR="XX"' /«PKGBUILDDIR»/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -S. -e'FMT/STR="XX"' /«PKGBUILDDIR»/test/view.filter.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -H -C5:nonmajor /tmp/hB2vxVgGqd/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -H -c6:nonmajor /tmp/hB2vxVgGqd/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -H -q0.3:major /tmp/hB2vxVgGqd/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/hB2vxVgGqd/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/hB2vxVgGqd/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /«PKGBUILDDIR»/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/hB2vxVgGqd/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call --no-version -mv /«PKGBUILDDIR»/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call -Ob -mv /«PKGBUILDDIR»/test/mpileup.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call --no-version -mg0 /«PKGBUILDDIR»/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call -Ob -mg0 /«PKGBUILDDIR»/test/mpileup.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call --no-version -mv --ploidy-file /«PKGBUILDDIR»/test/mpileup.ploidy -S /«PKGBUILDDIR»/test/mpileup.samples /«PKGBUILDDIR»/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call -Ob -mv --ploidy-file /«PKGBUILDDIR»/test/mpileup.ploidy -S /«PKGBUILDDIR»/test/mpileup.samples /«PKGBUILDDIR»/test/mpileup.X.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call --no-version -mv --ploidy-file /«PKGBUILDDIR»/test/mpileup.ploidy -S /«PKGBUILDDIR»/test/mpileup.ped /«PKGBUILDDIR»/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call -Ob -mv --ploidy-file /«PKGBUILDDIR»/test/mpileup.ploidy -S /«PKGBUILDDIR»/test/mpileup.ped /«PKGBUILDDIR»/test/mpileup.X.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call --no-version -mv --ploidy-file /«PKGBUILDDIR»/test/mpileup.ploidy -S /«PKGBUILDDIR»/test/mpileup.2.samples /«PKGBUILDDIR»/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call -Ob -mv --ploidy-file /«PKGBUILDDIR»/test/mpileup.ploidy -S /«PKGBUILDDIR»/test/mpileup.2.samples /«PKGBUILDDIR»/test/mpileup.X.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call_cAls:
+ /«PKGBUILDDIR»/bcftools call --no-version -mA -C alleles -T /tmp/hB2vxVgGqd/mpileup.tab.gz /«PKGBUILDDIR»/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call_cAls:
+ /«PKGBUILDDIR»/bcftools call -Ob -mA -C alleles -T /tmp/hB2vxVgGqd/mpileup.tab.gz /«PKGBUILDDIR»/test/mpileup.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call --no-version -cv /«PKGBUILDDIR»/test/mpileup.c.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call -Ob -cv /«PKGBUILDDIR»/test/mpileup.c.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call --no-version -cv --ploidy-file /«PKGBUILDDIR»/test/mpileup.ploidy -S /«PKGBUILDDIR»/test/mpileup.samples /«PKGBUILDDIR»/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call -Ob -cv --ploidy-file /«PKGBUILDDIR»/test/mpileup.ploidy -S /«PKGBUILDDIR»/test/mpileup.samples /«PKGBUILDDIR»/test/mpileup.c.X.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call --no-version -cv --ploidy-file /«PKGBUILDDIR»/test/mpileup.ploidy -S /«PKGBUILDDIR»/test/mpileup.ped /«PKGBUILDDIR»/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call -Ob -cv --ploidy-file /«PKGBUILDDIR»/test/mpileup.ploidy -S /«PKGBUILDDIR»/test/mpileup.ped /«PKGBUILDDIR»/test/mpileup.c.X.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call --no-version -cv --ploidy-file /«PKGBUILDDIR»/test/mpileup.ploidy -S /«PKGBUILDDIR»/test/mpileup.2.samples /«PKGBUILDDIR»/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /«PKGBUILDDIR»/bcftools call -Ob -cv --ploidy-file /«PKGBUILDDIR»/test/mpileup.ploidy -S /«PKGBUILDDIR»/test/mpileup.2.samples /«PKGBUILDDIR»/test/mpileup.c.X.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -mx -g2 -G2 /«PKGBUILDDIR»/test/filter.1.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -mx -g2 -G2 /«PKGBUILDDIR»/test/filter.1.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /«PKGBUILDDIR»/test/filter.2.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -e'DP=19' /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -e'DP=19' /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -e'DP=19' -s XX /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -e'DP=19' -s XX /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -e'DP=19' -s XX -m+ /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -e'DP=19' -s XX -m+ /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -e'DP=19' -s XX -mx /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -e'DP=19' -s XX -mx /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -e'DP=19' -s XX -m+x /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -e'DP=19' -s XX -m+x /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -e'FMT/GT="0/2"' /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -e'FMT/GT="0/2"' /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -e'FMT/GT="0/2"' -s XX /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -i'ALT="."' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -i'ALT="."' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -S . -i 'FORMAT/TEST3<25' /«PKGBUILDDIR»/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /«PKGBUILDDIR»/test/filter.4.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -S . -i 'FORMAT/TEST4<25' /«PKGBUILDDIR»/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /«PKGBUILDDIR»/test/filter.4.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -i'GT="A"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -i'GT="A"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -i'GT="RR"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -i'GT="RR"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -i'GT="RA"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -i'GT="RA"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -i'GT="AR"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -i'GT="AR"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -i'GT="AA"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -i'GT="AA"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -i'GT="aA"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -i'GT="aA"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -i'GT="Aa"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -i'GT="Aa"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -i'GT="HOM"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -i'GT="HOM"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -i'GT="HET"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -i'GT="HET"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -i'GT="HAP"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /«PKGBUILDDIR»/bcftools filter -Ob -i'GT="HAP"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_sort:
+ /«PKGBUILDDIR»/bcftools sort -m 0 /«PKGBUILDDIR»/test/sort.vcf | /«PKGBUILDDIR»/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.GQIGcA
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /«PKGBUILDDIR»/bcftools sort -Ob -m 0 /«PKGBUILDDIR»/test/sort.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.XTFgtE
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /«PKGBUILDDIR»/bcftools sort -m 1000 /«PKGBUILDDIR»/test/sort.vcf | /«PKGBUILDDIR»/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.BJkXbG
+Merging 3 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /«PKGBUILDDIR»/bcftools sort -Ob -m 1000 /«PKGBUILDDIR»/test/sort.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.Iwaq3F
+Merging 3 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_regions:
+ /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /«PKGBUILDDIR»/test/regions.tab /tmp/hB2vxVgGqd/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/regions.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /«PKGBUILDDIR»/test/regions.tab
+.. ok
+
+test_vcf_regions:
+ /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /«PKGBUILDDIR»/test/regions.tab /tmp/hB2vxVgGqd/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/hB2vxVgGqd/regions.tab.gz /tmp/hB2vxVgGqd/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/regions.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/hB2vxVgGqd/regions.tab.gz
+.. ok
+
+test_vcf_regions:
+ /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/hB2vxVgGqd/regions.tab.gz /tmp/hB2vxVgGqd/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/hB2vxVgGqd/regions.bed /tmp/hB2vxVgGqd/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/regions.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/hB2vxVgGqd/regions.bed
+.. ok
+
+test_vcf_regions:
+ /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/hB2vxVgGqd/regions.bed /tmp/hB2vxVgGqd/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/hB2vxVgGqd/regions.bed.gz /tmp/hB2vxVgGqd/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/regions.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/hB2vxVgGqd/regions.bed.gz
+.. ok
+
+test_vcf_regions:
+ /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/hB2vxVgGqd/regions.bed.gz /tmp/hB2vxVgGqd/regions.vcf.gz
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -a /tmp/hB2vxVgGqd/annotate.tab.gz -h /«PKGBUILDDIR»/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /«PKGBUILDDIR»/test/annotate.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/hB2vxVgGqd/annotate.tab.gz -h /«PKGBUILDDIR»/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /«PKGBUILDDIR»/test/annotate.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -a /tmp/hB2vxVgGqd/annotate2.tab.gz -h /«PKGBUILDDIR»/test/annotate.hdr -c CHROM,FROM,TO,T_STR /«PKGBUILDDIR»/test/annotate.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/hB2vxVgGqd/annotate2.tab.gz -h /«PKGBUILDDIR»/test/annotate.hdr -c CHROM,FROM,TO,T_STR /«PKGBUILDDIR»/test/annotate.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -a /tmp/hB2vxVgGqd/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/hB2vxVgGqd/annotate.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/hB2vxVgGqd/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/hB2vxVgGqd/annotate.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -a /tmp/hB2vxVgGqd/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/hB2vxVgGqd/annotate2.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/annotate4.out
+ /«PKGBUILDDIR»/test/annotate4.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/hB2vxVgGqd/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/hB2vxVgGqd/annotate2.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/annotate4.out
+ /«PKGBUILDDIR»/test/annotate4.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -a /tmp/hB2vxVgGqd/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/hB2vxVgGqd/annotate2.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/hB2vxVgGqd/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/hB2vxVgGqd/annotate2.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /«PKGBUILDDIR»/test/annotate3.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /«PKGBUILDDIR»/test/annotate3.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -x FORMAT /«PKGBUILDDIR»/test/annotate3.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -x FORMAT /«PKGBUILDDIR»/test/annotate3.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -a /tmp/hB2vxVgGqd/annots4.vcf.gz -c +INFO /tmp/hB2vxVgGqd/annotate4.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/annotate8.out
+ /«PKGBUILDDIR»/test/annotate8.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/hB2vxVgGqd/annots4.vcf.gz -c +INFO /tmp/hB2vxVgGqd/annotate4.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/annotate8.out
+ /«PKGBUILDDIR»/test/annotate8.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -a /tmp/hB2vxVgGqd/annots4.tab.gz -h /«PKGBUILDDIR»/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /«PKGBUILDDIR»/test/annotate4.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/annotate8.out
+ /«PKGBUILDDIR»/test/annotate8.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/hB2vxVgGqd/annots4.tab.gz -h /«PKGBUILDDIR»/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /«PKGBUILDDIR»/test/annotate4.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/annotate8.out
+ /«PKGBUILDDIR»/test/annotate8.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -a /tmp/hB2vxVgGqd/annots10.tab.gz -h /«PKGBUILDDIR»/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /«PKGBUILDDIR»/test/annotate10.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/annotate10.out
+ /«PKGBUILDDIR»/test/annotate10.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/hB2vxVgGqd/annots10.tab.gz -h /«PKGBUILDDIR»/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /«PKGBUILDDIR»/test/annotate10.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/annotate10.out
+ /«PKGBUILDDIR»/test/annotate10.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -a /tmp/hB2vxVgGqd/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/hB2vxVgGqd/annotate2.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/annotate11.out
+ /«PKGBUILDDIR»/test/annotate11.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/hB2vxVgGqd/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/hB2vxVgGqd/annotate2.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/annotate11.out
+ /«PKGBUILDDIR»/test/annotate11.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -a /tmp/hB2vxVgGqd/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /«PKGBUILDDIR»/test/annotate2.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/annotate11.out
+ /«PKGBUILDDIR»/test/annotate11.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/hB2vxVgGqd/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /«PKGBUILDDIR»/test/annotate2.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/annotate11.out
+ /«PKGBUILDDIR»/test/annotate11.out.new
+.. failed ...
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -a /tmp/hB2vxVgGqd/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/hB2vxVgGqd/annotate2.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/hB2vxVgGqd/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/hB2vxVgGqd/annotate2.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -a /tmp/hB2vxVgGqd/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/hB2vxVgGqd/annotate2.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/hB2vxVgGqd/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/hB2vxVgGqd/annotate2.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +missing2ref --no-version /tmp/hB2vxVgGqd/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +missing2ref --no-version /tmp/hB2vxVgGqd/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +setGT --no-version /tmp/hB2vxVgGqd/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +setGT --no-version /tmp/hB2vxVgGqd/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +setGT --no-version /tmp/hB2vxVgGqd/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +setGT --no-version /tmp/hB2vxVgGqd/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -a /tmp/hB2vxVgGqd/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /«PKGBUILDDIR»/test/annotate9.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/hB2vxVgGqd/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /«PKGBUILDDIR»/test/annotate9.vcf 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-AN-AC --no-version /tmp/hB2vxVgGqd/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-AN-AC --no-version /tmp/hB2vxVgGqd/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +dosage /tmp/hB2vxVgGqd/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +dosage /tmp/hB2vxVgGqd/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fixploidy --no-version /tmp/hB2vxVgGqd/fixploidy.vcf.gz -- -s /«PKGBUILDDIR»/test/fixploidy.samples -p /«PKGBUILDDIR»/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fixploidy --no-version /tmp/hB2vxVgGqd/fixploidy.bcf -- -s /«PKGBUILDDIR»/test/fixploidy.samples -p /«PKGBUILDDIR»/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +guess-ploidy /tmp/hB2vxVgGqd/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +guess-ploidy /tmp/hB2vxVgGqd/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +guess-ploidy /tmp/hB2vxVgGqd/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/guess-ploidy.GL.out
+ /«PKGBUILDDIR»/test/guess-ploidy.GL.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +guess-ploidy /tmp/hB2vxVgGqd/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/guess-ploidy.GL.out
+ /«PKGBUILDDIR»/test/guess-ploidy.GL.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +tag2tag --no-version /tmp/hB2vxVgGqd/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +tag2tag --no-version /tmp/hB2vxVgGqd/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +tag2tag --no-version /tmp/hB2vxVgGqd/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +tag2tag --no-version /tmp/hB2vxVgGqd/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-tags --no-version /tmp/hB2vxVgGqd/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-tags --no-version /tmp/hB2vxVgGqd/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-tags --no-version /tmp/hB2vxVgGqd/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-tags --no-version /tmp/hB2vxVgGqd/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-tags --no-version /tmp/hB2vxVgGqd/view.vcf.gz -- -t AC -S /«PKGBUILDDIR»/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-tags --no-version /tmp/hB2vxVgGqd/view.bcf -- -t AC -S /«PKGBUILDDIR»/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-tags --no-version /tmp/hB2vxVgGqd/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-tags --no-version /tmp/hB2vxVgGqd/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-tags --no-version /tmp/hB2vxVgGqd/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-tags --no-version /tmp/hB2vxVgGqd/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTisec /tmp/hB2vxVgGqd/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +trio-switch-rate /tmp/hB2vxVgGqd/trio.vcf.gz -- -p /«PKGBUILDDIR»/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +trio-switch-rate /tmp/hB2vxVgGqd/trio.bcf -- -p /«PKGBUILDDIR»/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +ad-bias /tmp/hB2vxVgGqd/ad-bias.vcf.gz -- -s /«PKGBUILDDIR»/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +ad-bias /tmp/hB2vxVgGqd/ad-bias.bcf -- -s /«PKGBUILDDIR»/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +af-dist /tmp/hB2vxVgGqd/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +af-dist /tmp/hB2vxVgGqd/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fixref /tmp/hB2vxVgGqd/fixref.2a.vcf.gz -- -f /«PKGBUILDDIR»/test/norm.fa -i /tmp/hB2vxVgGqd/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fixref /tmp/hB2vxVgGqd/fixref.2a.bcf -- -f /«PKGBUILDDIR»/test/norm.fa -i /tmp/hB2vxVgGqd/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-from-fasta /tmp/hB2vxVgGqd/aa.vcf.gz -- -f /«PKGBUILDDIR»/test/aa.fa -c AA -h /«PKGBUILDDIR»/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-from-fasta /tmp/hB2vxVgGqd/aa.bcf -- -f /«PKGBUILDDIR»/test/aa.fa -c AA -h /«PKGBUILDDIR»/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-from-fasta /tmp/hB2vxVgGqd/ref.vcf.gz -- -f /«PKGBUILDDIR»/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +fill-from-fasta /tmp/hB2vxVgGqd/ref.bcf -- -f /«PKGBUILDDIR»/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTsubset --no-version /tmp/hB2vxVgGqd/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTsubset --no-version /tmp/hB2vxVgGqd/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTsubset --no-version /tmp/hB2vxVgGqd/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTsubset --no-version /tmp/hB2vxVgGqd/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTsubset --no-version /tmp/hB2vxVgGqd/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +GTsubset --no-version /tmp/hB2vxVgGqd/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +mendelian --no-version /tmp/hB2vxVgGqd/mendelian.vcf.gz -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +mendelian --no-version /tmp/hB2vxVgGqd/mendelian.bcf -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +mendelian --no-version /tmp/hB2vxVgGqd/mendelian.vcf.gz -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +mendelian --no-version /tmp/hB2vxVgGqd/mendelian.bcf -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +mendelian --no-version /tmp/hB2vxVgGqd/mendelian.vcf.gz -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /«PKGBUILDDIR»/bcftools +mendelian --no-version /tmp/hB2vxVgGqd/mendelian.bcf -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat --no-version /tmp/hB2vxVgGqd/concat.1.a.vcf.gz /tmp/hB2vxVgGqd/concat.1.b.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat -Ob /tmp/hB2vxVgGqd/concat.1.a.vcf.gz /tmp/hB2vxVgGqd/concat.1.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat --no-version /tmp/hB2vxVgGqd/concat.1.a.bcf /tmp/hB2vxVgGqd/concat.1.b.bcf
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat -Ob /tmp/hB2vxVgGqd/concat.1.a.bcf /tmp/hB2vxVgGqd/concat.1.b.bcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat --no-version -a /tmp/hB2vxVgGqd/concat.2.a.vcf.gz /tmp/hB2vxVgGqd/concat.2.b.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat -Ob -a /tmp/hB2vxVgGqd/concat.2.a.vcf.gz /tmp/hB2vxVgGqd/concat.2.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat --no-version -a /tmp/hB2vxVgGqd/concat.2.a.bcf /tmp/hB2vxVgGqd/concat.2.b.bcf
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat -Ob -a /tmp/hB2vxVgGqd/concat.2.a.bcf /tmp/hB2vxVgGqd/concat.2.b.bcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat --no-version -aD /tmp/hB2vxVgGqd/concat.2.a.vcf.gz /tmp/hB2vxVgGqd/concat.2.b.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat -Ob -aD /tmp/hB2vxVgGqd/concat.2.a.vcf.gz /tmp/hB2vxVgGqd/concat.2.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat --no-version -aD /tmp/hB2vxVgGqd/concat.2.a.bcf /tmp/hB2vxVgGqd/concat.2.b.bcf
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat -Ob -aD /tmp/hB2vxVgGqd/concat.2.a.bcf /tmp/hB2vxVgGqd/concat.2.b.bcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat --no-version -l /tmp/hB2vxVgGqd/concat.3.a.vcf.gz /tmp/hB2vxVgGqd/concat.3.b.vcf.gz /tmp/hB2vxVgGqd/concat.3.0.vcf.gz /tmp/hB2vxVgGqd/concat.3.c.vcf.gz /tmp/hB2vxVgGqd/concat.3.d.vcf.gz /tmp/hB2vxVgGqd/concat.3.e.vcf.gz /tmp/hB2vxVgGqd/concat.3.f.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat -Ob -l /tmp/hB2vxVgGqd/concat.3.a.vcf.gz /tmp/hB2vxVgGqd/concat.3.b.vcf.gz /tmp/hB2vxVgGqd/concat.3.0.vcf.gz /tmp/hB2vxVgGqd/concat.3.c.vcf.gz /tmp/hB2vxVgGqd/concat.3.d.vcf.gz /tmp/hB2vxVgGqd/concat.3.e.vcf.gz /tmp/hB2vxVgGqd/concat.3.f.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat --no-version -l /tmp/hB2vxVgGqd/concat.3.a.bcf /tmp/hB2vxVgGqd/concat.3.b.bcf /tmp/hB2vxVgGqd/concat.3.0.bcf /tmp/hB2vxVgGqd/concat.3.c.bcf /tmp/hB2vxVgGqd/concat.3.d.bcf /tmp/hB2vxVgGqd/concat.3.e.bcf /tmp/hB2vxVgGqd/concat.3.f.bcf
+.. ok
+
+test_vcf_concat:
+ /«PKGBUILDDIR»/bcftools concat -Ob -l /tmp/hB2vxVgGqd/concat.3.a.bcf /tmp/hB2vxVgGqd/concat.3.b.bcf /tmp/hB2vxVgGqd/concat.3.0.bcf /tmp/hB2vxVgGqd/concat.3.c.bcf /tmp/hB2vxVgGqd/concat.3.d.bcf /tmp/hB2vxVgGqd/concat.3.e.bcf /tmp/hB2vxVgGqd/concat.3.f.bcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+Random seed for test_naive_concat: 3096983409
+.. ok
+
+test_naive_concat:
+ /«PKGBUILDDIR»/bcftools concat --naive /tmp/hB2vxVgGqd/naive_concat.0.bcf /tmp/hB2vxVgGqd/naive_concat.1.bcf /tmp/hB2vxVgGqd/naive_concat.2.bcf /tmp/hB2vxVgGqd/naive_concat.3.bcf /tmp/hB2vxVgGqd/naive_concat.4.bcf /tmp/hB2vxVgGqd/naive_concat.5.bcf /tmp/hB2vxVgGqd/naive_concat.6.bcf /tmp/hB2vxVgGqd/naive_concat.7.bcf /tmp/hB2vxVgGqd/naive_concat.8.bcf /tmp/hB2vxVgGqd/naive_concat.9.bcf | /«PKGBUILDDIR»/bcftools view -H
+.. ok
+
+test_naive_concat:
+ /«PKGBUILDDIR»/bcftools concat --naive /tmp/hB2vxVgGqd/naive_concat.0.vcf.gz /tmp/hB2vxVgGqd/naive_concat.1.vcf.gz /tmp/hB2vxVgGqd/naive_concat.2.vcf.gz /tmp/hB2vxVgGqd/naive_concat.3.vcf.gz /tmp/hB2vxVgGqd/naive_concat.4.vcf.gz /tmp/hB2vxVgGqd/naive_concat.5.vcf.gz /tmp/hB2vxVgGqd/naive_concat.6.vcf.gz /tmp/hB2vxVgGqd/naive_concat.7.vcf.gz /tmp/hB2vxVgGqd/naive_concat.8.vcf.gz /tmp/hB2vxVgGqd/naive_concat.9.vcf.gz | /«PKGBUILDDIR»/bcftools view -H
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.hdr /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.hdr | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.hdr /tmp/hB2vxVgGqd/reheader.bcf | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/hB2vxVgGqd/reheader.bcf | /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.hdr | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.hdr /tmp/hB2vxVgGqd/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/hB2vxVgGqd/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.hdr | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples /tmp/hB2vxVgGqd/reheader.bcf | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/hB2vxVgGqd/reheader.bcf | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples /tmp/hB2vxVgGqd/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/hB2vxVgGqd/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples2 /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples2 | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples2 /tmp/hB2vxVgGqd/reheader.bcf | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/hB2vxVgGqd/reheader.bcf | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples2 | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples2 /tmp/hB2vxVgGqd/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/hB2vxVgGqd/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples2 | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples3 /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples3 | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples3 /tmp/hB2vxVgGqd/reheader.bcf | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/hB2vxVgGqd/reheader.bcf | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples3 | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples3 /tmp/hB2vxVgGqd/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/hB2vxVgGqd/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples3 | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples4 /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples4 | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples4 /tmp/hB2vxVgGqd/reheader.bcf | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/hB2vxVgGqd/reheader.bcf | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples4 | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples4 /tmp/hB2vxVgGqd/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/hB2vxVgGqd/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples4 | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.empty.hdr /«PKGBUILDDIR»/test/empty.vcf | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /«PKGBUILDDIR»/test/empty.vcf | /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.empty.hdr | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.empty.hdr /tmp/hB2vxVgGqd/empty.bcf | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/hB2vxVgGqd/empty.bcf | /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.empty.hdr | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.empty.hdr /tmp/hB2vxVgGqd/empty.vcf.gz | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/hB2vxVgGqd/empty.vcf.gz | /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.empty.hdr | /«PKGBUILDDIR»/bcftools view --no-version
+.. ok
+
+test_rename_chrs:
+ /«PKGBUILDDIR»/bcftools annotate --rename-chrs /tmp/hB2vxVgGqd/rename.map -Ov /tmp/hB2vxVgGqd/annotate.bcf | /«PKGBUILDDIR»/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /«PKGBUILDDIR»/bcftools annotate --rename-chrs /tmp/hB2vxVgGqd/rename.map -Ob /tmp/hB2vxVgGqd/annotate.bcf | /«PKGBUILDDIR»/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /«PKGBUILDDIR»/bcftools annotate --rename-chrs /tmp/hB2vxVgGqd/rename.map -Ov /«PKGBUILDDIR»/test/annotate.vcf | /«PKGBUILDDIR»/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /«PKGBUILDDIR»/bcftools annotate --rename-chrs /tmp/hB2vxVgGqd/rename.map -Ob /«PKGBUILDDIR»/test/annotate.vcf | /«PKGBUILDDIR»/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert -g -,. /tmp/hB2vxVgGqd/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert -g .,- /tmp/hB2vxVgGqd/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g .,- 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert -g -,. --tag PL /tmp/hB2vxVgGqd/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g -,. --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert -g .,- --tag PL /tmp/hB2vxVgGqd/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g .,- --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert -g -,. --vcf-ids /tmp/hB2vxVgGqd/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/check.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g -,. --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert -g .,- --vcf-ids /tmp/hB2vxVgGqd/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/check.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g .,- --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert -g -,. --chrom /tmp/hB2vxVgGqd/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/check.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g -,. --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert -g .,- --chrom /tmp/hB2vxVgGqd/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/check.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g .,- --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert -g -,. --chrom --vcf-ids /tmp/hB2vxVgGqd/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/check.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert -g .,- --chrom --vcf-ids /tmp/hB2vxVgGqd/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/check.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert -h -,.,. /tmp/hB2vxVgGqd/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -h -,.,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert -h .,-,. /tmp/hB2vxVgGqd/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -h .,-,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert -h .,.,- /tmp/hB2vxVgGqd/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -h .,.,- 2>/dev/null
+.. ok
+
+test_vcf_convert_hls2vcf:
+ /«PKGBUILDDIR»/bcftools convert -H /«PKGBUILDDIR»/test/convert.hls.gt.hap,/«PKGBUILDDIR»/test/convert.hls.gt.legend,/«PKGBUILDDIR»/test/convert.hls.gt.samples 2>/dev/null | grep -v ^##
+.. ok
+
+test_vcf_convert_hls2vcf:
+ /«PKGBUILDDIR»/bcftools convert -H /«PKGBUILDDIR»/test/convert.hls.gt.hap,/«PKGBUILDDIR»/test/convert.hls.gt.legend,/«PKGBUILDDIR»/test/convert.hls.gt.samples -Ou 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##
+.. ok
+
+test_vcf_convert_hs2vcf:
+ /«PKGBUILDDIR»/bcftools convert --hapsample2vcf /«PKGBUILDDIR»/test/convert.hs.gt.hap,/«PKGBUILDDIR»/test/convert.hs.gt.samples 2>/dev/null | grep -v ^##
+.. ok
+
+test_vcf_convert_hs2vcf:
+ /«PKGBUILDDIR»/bcftools convert --hapsample2vcf /«PKGBUILDDIR»/test/convert.hs.gt.hap,/«PKGBUILDDIR»/test/convert.hs.gt.samples -Ou 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert --hapsample -,. /tmp/hB2vxVgGqd/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert --hapsample -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools convert --hapsample .,- /tmp/hB2vxVgGqd/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert --hapsample .,- 2>/dev/null
+.. ok
+
+test_vcf_convert_gvcf:
+ /«PKGBUILDDIR»/bcftools convert --no-version --gvcf2vcf -f /«PKGBUILDDIR»/test/gvcf.fa /tmp/hB2vxVgGqd/convert.gvcf.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert_gvcf:
+ /«PKGBUILDDIR»/bcftools view -Ob /tmp/hB2vxVgGqd/convert.gvcf.vcf.gz | /«PKGBUILDDIR»/bcftools convert --gvcf2vcf -f /«PKGBUILDDIR»/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools
+.. ok
+
+test_vcf_convert_tsv2vcf:
+ /«PKGBUILDDIR»/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /«PKGBUILDDIR»/test/23andme.fa --tsv2vcf /«PKGBUILDDIR»/test/convert.23andme 2>/dev/null
+.. ok
+
+test_vcf_convert_tsv2vcf:
+ /«PKGBUILDDIR»/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /«PKGBUILDDIR»/test/23andme.fa --tsv2vcf /«PKGBUILDDIR»/test/convert.23andme 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_consensus:
+ /«PKGBUILDDIR»/bcftools consensus /tmp/hB2vxVgGqd/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -m /«PKGBUILDDIR»/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /«PKGBUILDDIR»/bcftools consensus /tmp/hB2vxVgGqd/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -m /«PKGBUILDDIR»/test/consensus.tab -c /tmp/hB2vxVgGqd/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/hB2vxVgGqd/consensus.1.chain.new
+.. ok
+
+test_vcf_consensus:
+ /«PKGBUILDDIR»/bcftools consensus /tmp/hB2vxVgGqd/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -H 1 -m /«PKGBUILDDIR»/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /«PKGBUILDDIR»/bcftools consensus /tmp/hB2vxVgGqd/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -H 1 -m /«PKGBUILDDIR»/test/consensus.tab -c /tmp/hB2vxVgGqd/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/hB2vxVgGqd/consensus.2.chain.new
+.. ok
+
+test_vcf_consensus:
+ /«PKGBUILDDIR»/bcftools consensus /tmp/hB2vxVgGqd/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -I -m /«PKGBUILDDIR»/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /«PKGBUILDDIR»/bcftools consensus /tmp/hB2vxVgGqd/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -I -m /«PKGBUILDDIR»/test/consensus.tab -c /tmp/hB2vxVgGqd/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/hB2vxVgGqd/consensus.3.chain.new
+.. ok
+
+test_vcf_consensus:
+ /«PKGBUILDDIR»/bcftools consensus /tmp/hB2vxVgGqd/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /«PKGBUILDDIR»/bcftools consensus /tmp/hB2vxVgGqd/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -H 1 -c /tmp/hB2vxVgGqd/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/hB2vxVgGqd/consensus.4.chain.new
+.. ok
+
+test_vcf_consensus:
+ /«PKGBUILDDIR»/bcftools consensus /tmp/hB2vxVgGqd/consensus2.vcf.gz -f /«PKGBUILDDIR»/test/consensus2.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /«PKGBUILDDIR»/bcftools consensus /tmp/hB2vxVgGqd/consensus2.vcf.gz -f /«PKGBUILDDIR»/test/consensus2.fa -H 2 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /«PKGBUILDDIR»/bcftools consensus /tmp/hB2vxVgGqd/empty.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa 2>/dev/null
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -b /tmp/hB2vxVgGqd/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob -b /tmp/hB2vxVgGqd/mpileup.bam.urllist 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -b /tmp/hB2vxVgGqd/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob -b /tmp/hB2vxVgGqd/mpileup.cram.urllist 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,DV -r17:100-600 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,DV -r17:100-600 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,DV -r17:100-600 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,DV -r17:100-600 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/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 /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/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 /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/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 /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/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 /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -S /«PKGBUILDDIR»/test/mplp.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -S /«PKGBUILDDIR»/test/mplp.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -S /«PKGBUILDDIR»/test/mplp.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -S /«PKGBUILDDIR»/test/mplp.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -S ^/«PKGBUILDDIR»/test/mplp.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -S ^/«PKGBUILDDIR»/test/mplp.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -S ^/«PKGBUILDDIR»/test/mplp.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -r17:100-150 -S ^/«PKGBUILDDIR»/test/mplp.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -t17:100-150 -S /«PKGBUILDDIR»/test/mplp.9.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -t17:100-150 -S /«PKGBUILDDIR»/test/mplp.9.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -t17:100-150 -S /«PKGBUILDDIR»/test/mplp.9.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -t17:100-150 -S /«PKGBUILDDIR»/test/mplp.9.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -t17:100-150 -G /«PKGBUILDDIR»/test/mplp.10.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -t17:100-150 -G /«PKGBUILDDIR»/test/mplp.10.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.bam /«PKGBUILDDIR»/test/mpileup/mpileup.2.bam /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -t17:100-150 -G /«PKGBUILDDIR»/test/mplp.10.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -t17:100-150 -G /«PKGBUILDDIR»/test/mplp.10.samples -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.1.cram /«PKGBUILDDIR»/test/mpileup/mpileup.2.cram /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -s HG00102 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam /«PKGBUILDDIR»/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -s HG00102 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam /«PKGBUILDDIR»/test/mpileup/mpileup.4.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -s HG00102 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram /«PKGBUILDDIR»/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -s HG00102 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram /«PKGBUILDDIR»/test/mpileup/mpileup.4.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -s ^HG99999 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam /«PKGBUILDDIR»/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -s ^HG99999 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam /«PKGBUILDDIR»/test/mpileup/mpileup.4.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -s ^HG99999 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram /«PKGBUILDDIR»/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -s ^HG99999 -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram /«PKGBUILDDIR»/test/mpileup/mpileup.4.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -G /«PKGBUILDDIR»/test/mplp.11.rgs -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam /«PKGBUILDDIR»/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -G /«PKGBUILDDIR»/test/mplp.11.rgs -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam /«PKGBUILDDIR»/test/mpileup/mpileup.4.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -G /«PKGBUILDDIR»/test/mplp.11.rgs -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram /«PKGBUILDDIR»/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -G /«PKGBUILDDIR»/test/mplp.11.rgs -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram /«PKGBUILDDIR»/test/mpileup/mpileup.4.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -G /«PKGBUILDDIR»/test/mplp.11.rgs -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam /«PKGBUILDDIR»/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -G /«PKGBUILDDIR»/test/mplp.11.rgs -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.3.bam /«PKGBUILDDIR»/test/mpileup/mpileup.4.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -G /«PKGBUILDDIR»/test/mplp.11.rgs -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram /«PKGBUILDDIR»/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -G /«PKGBUILDDIR»/test/mplp.11.rgs -f /«PKGBUILDDIR»/test/mpileup/mpileup.ref.fa -Ob /«PKGBUILDDIR»/test/mpileup/mpileup.3.cram /«PKGBUILDDIR»/test/mpileup/mpileup.4.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out
+ /«PKGBUILDDIR»/test/mpileup/mpileup.11.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a AD -f /«PKGBUILDDIR»/test/mpileup/indel-AD.1.fa /«PKGBUILDDIR»/test/mpileup/indel-AD.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/indel-AD.1.out
+ /«PKGBUILDDIR»/test/mpileup/indel-AD.1.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a AD -f /«PKGBUILDDIR»/test/mpileup/indel-AD.1.fa -Ob /«PKGBUILDDIR»/test/mpileup/indel-AD.1.bam 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/indel-AD.1.out
+ /«PKGBUILDDIR»/test/mpileup/indel-AD.1.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a AD -f /«PKGBUILDDIR»/test/mpileup/indel-AD.1.fa /«PKGBUILDDIR»/test/mpileup/indel-AD.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/indel-AD.1.out
+ /«PKGBUILDDIR»/test/mpileup/indel-AD.1.out.new
+.. failed ...
+
+test_mpileup:
+ /«PKGBUILDDIR»/bcftools mpileup -a AD -f /«PKGBUILDDIR»/test/mpileup/indel-AD.1.fa -Ob /«PKGBUILDDIR»/test/mpileup/indel-AD.1.cram 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /«PKGBUILDDIR»/test/mpileup/indel-AD.1.out
+ /«PKGBUILDDIR»/test/mpileup/indel-AD.1.out.new
+.. failed ...
+
+test_csq:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq.fa -g /«PKGBUILDDIR»/test/csq.gff3 /«PKGBUILDDIR»/test/csq.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq.gff3 ...
+Indexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENSG00000173376/ENSG00000173376.fa -g /«PKGBUILDDIR»/test/csq/ENSG00000173376/ENSG00000173376.gff /«PKGBUILDDIR»/test/csq/ENSG00000173376/synon.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENSG00000173376/ENSG00000173376.gff ...
+Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000218032/ENST00000218032.fa -g /«PKGBUILDDIR»/test/csq/ENST00000218032/ENST00000218032.gff /«PKGBUILDDIR»/test/csq/ENST00000218032/start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000218032/ENST00000218032.fa -g /«PKGBUILDDIR»/test/csq/ENST00000218032/ENST00000218032.gff /«PKGBUILDDIR»/test/csq/ENST00000218032/start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000227471/ENST00000227471.fa -g /«PKGBUILDDIR»/test/csq/ENST00000227471/ENST00000227471.gff /«PKGBUILDDIR»/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000227471/ENST00000227471.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000256452/ENST00000256452.fa -g /«PKGBUILDDIR»/test/csq/ENST00000256452/ENST00000256452.gff /«PKGBUILDDIR»/test/csq/ENST00000256452/intron.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000256452/ENST00000256452.gff ...
+Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000294661/ENST00000294661.fa -g /«PKGBUILDDIR»/test/csq/ENST00000294661/ENST00000294661.gff /«PKGBUILDDIR»/test/csq/ENST00000294661/non-coding-boundary.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000294661/ENST00000294661.fa -g /«PKGBUILDDIR»/test/csq/ENST00000294661/ENST00000294661.gff /«PKGBUILDDIR»/test/csq/ENST00000294661/non-coding-boundary.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000295641/ENST00000295641.fa -g /«PKGBUILDDIR»/test/csq/ENST00000295641/ENST00000295641.gff /«PKGBUILDDIR»/test/csq/ENST00000295641/not-a-start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000295641/ENST00000295641.fa -g /«PKGBUILDDIR»/test/csq/ENST00000295641/ENST00000295641.gff /«PKGBUILDDIR»/test/csq/ENST00000295641/not-a-start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000301246/ENST00000301246.fa -g /«PKGBUILDDIR»/test/csq/ENST00000301246/ENST00000301246.gff /«PKGBUILDDIR»/test/csq/ENST00000301246/15bp-insert.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000301246/ENST00000301246.gff ...
+Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000303039/ENST00000303039.fa -g /«PKGBUILDDIR»/test/csq/ENST00000303039/ENST00000303039.gff /«PKGBUILDDIR»/test/csq/ENST00000303039/not-a-stop.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000303039/ENST00000303039.fa -g /«PKGBUILDDIR»/test/csq/ENST00000303039/ENST00000303039.gff /«PKGBUILDDIR»/test/csq/ENST00000303039/not-a-stop.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000318249/ENST00000318249.fa -g /«PKGBUILDDIR»/test/csq/ENST00000318249/ENST00000318249.gff /«PKGBUILDDIR»/test/csq/ENST00000318249/start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000318249/ENST00000318249.fa -g /«PKGBUILDDIR»/test/csq/ENST00000318249/ENST00000318249.gff /«PKGBUILDDIR»/test/csq/ENST00000318249/start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000329454/ENST00000329454.fa -g /«PKGBUILDDIR»/test/csq/ENST00000329454/ENST00000329454.gff /«PKGBUILDDIR»/test/csq/ENST00000329454/boundary-deletion.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000329454/ENST00000329454.fa -g /«PKGBUILDDIR»/test/csq/ENST00000329454/ENST00000329454.gff /«PKGBUILDDIR»/test/csq/ENST00000329454/boundary-deletion.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/frame1.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/frame1.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/frame2.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/frame2.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/frame3.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/frame3.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/not-a-start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/not-a-start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.fa -g /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff /«PKGBUILDDIR»/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000357367/ENST00000357367.fa -g /«PKGBUILDDIR»/test/csq/ENST00000357367/ENST00000357367.gff /«PKGBUILDDIR»/test/csq/ENST00000357367/stop-retained.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000357367/ENST00000357367.gff ...
+Indexed 1 transcripts, 4 exons, 3 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000368801/ENST00000368801.fa -g /«PKGBUILDDIR»/test/csq/ENST00000368801/ENST00000368801.gff /«PKGBUILDDIR»/test/csq/ENST00000368801/compound-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000368801/ENST00000368801.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000373833/ENST00000373833.fa -g /«PKGBUILDDIR»/test/csq/ENST00000373833/ENST00000373833.gff /«PKGBUILDDIR»/test/csq/ENST00000373833/boundary-insertion.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000373833/ENST00000373833.fa -g /«PKGBUILDDIR»/test/csq/ENST00000373833/ENST00000373833.gff /«PKGBUILDDIR»/test/csq/ENST00000373833/boundary-insertion.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000375992/ENST00000375992.fa -g /«PKGBUILDDIR»/test/csq/ENST00000375992/ENST00000375992.gff /«PKGBUILDDIR»/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000375992/ENST00000375992.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000378322/ENST00000378322.fa -g /«PKGBUILDDIR»/test/csq/ENST00000378322/ENST00000378322.gff /«PKGBUILDDIR»/test/csq/ENST00000378322/end-overlap-tscript.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000378322/ENST00000378322.fa -g /«PKGBUILDDIR»/test/csq/ENST00000378322/ENST00000378322.gff /«PKGBUILDDIR»/test/csq/ENST00000378322/end-overlap-tscript.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000381157/ENST00000381157.fa -g /«PKGBUILDDIR»/test/csq/ENST00000381157/ENST00000381157.gff /«PKGBUILDDIR»/test/csq/ENST00000381157/haploid-diploid.vcf | /«PKGBUILDDIR»/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000381157/ENST00000381157.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 0 UTRs
+Calling...
+Warning: Skipping site with non-diploid/non-haploid genotypes at X:31180 C>T
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000382647/ENST00000382647.fa -g /«PKGBUILDDIR»/test/csq/ENST00000382647/ENST00000382647.gff /«PKGBUILDDIR»/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000382647/ENST00000382647.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000390520/ENST00000390520.fa -g /«PKGBUILDDIR»/test/csq/ENST00000390520/ENST00000390520.gff /«PKGBUILDDIR»/test/csq/ENST00000390520/deletion-overlap.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000390520/ENST00000390520.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000409523/ENST00000409523.fa -g /«PKGBUILDDIR»/test/csq/ENST00000409523/ENST00000409523.gff /«PKGBUILDDIR»/test/csq/ENST00000409523/long-overlapping-del.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000409523/ENST00000409523.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000410009/ENST00000410009.fa -g /«PKGBUILDDIR»/test/csq/ENST00000410009/ENST00000410009.gff /«PKGBUILDDIR»/test/csq/ENST00000410009/frameshift.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000410009/ENST00000410009.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000413103/ENST00000413103.fa -g /«PKGBUILDDIR»/test/csq/ENST00000413103/ENST00000413103.gff /«PKGBUILDDIR»/test/csq/ENST00000413103/long-deletion.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000413103/ENST00000413103.gff ...
+Indexed 1 transcripts, 2 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000420670/ENST00000420670.fa -g /«PKGBUILDDIR»/test/csq/ENST00000420670/ENST00000420670.gff /«PKGBUILDDIR»/test/csq/ENST00000420670/start-stop-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000420670/ENST00000420670.gff ...
+Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000423372/ENST00000423372.fa -g /«PKGBUILDDIR»/test/csq/ENST00000423372/ENST00000423372.gff /«PKGBUILDDIR»/test/csq/ENST00000423372/insert3.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000423372/ENST00000423372.fa -g /«PKGBUILDDIR»/test/csq/ENST00000423372/ENST00000423372.gff /«PKGBUILDDIR»/test/csq/ENST00000423372/insert3.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000423372/ENST00000423372.fa -g /«PKGBUILDDIR»/test/csq/ENST00000423372/ENST00000423372.gff /«PKGBUILDDIR»/test/csq/ENST00000423372/snps.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000423372/ENST00000423372.fa -g /«PKGBUILDDIR»/test/csq/ENST00000423372/ENST00000423372.gff /«PKGBUILDDIR»/test/csq/ENST00000423372/snps.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000436063/ENST00000436063.fa -g /«PKGBUILDDIR»/test/csq/ENST00000436063/ENST00000436063.gff /«PKGBUILDDIR»/test/csq/ENST00000436063/insert-before-utr.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000436063/ENST00000436063.gff ...
+Indexed 1 transcripts, 7 exons, 7 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000448695/ENST00000448695.fa -g /«PKGBUILDDIR»/test/csq/ENST00000448695/ENST00000448695.gff /«PKGBUILDDIR»/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000448695/ENST00000448695.gff ...
+Indexed 1 transcripts, 26 exons, 26 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000479739/ENST00000479739.fa -g /«PKGBUILDDIR»/test/csq/ENST00000479739/ENST00000479739.gff /«PKGBUILDDIR»/test/csq/ENST00000479739/short-cds-start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000479739/ENST00000479739.fa -g /«PKGBUILDDIR»/test/csq/ENST00000479739/ENST00000479739.gff /«PKGBUILDDIR»/test/csq/ENST00000479739/short-cds-start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000519442/ENST00000519442.fa -g /«PKGBUILDDIR»/test/csq/ENST00000519442/ENST00000519442.gff /«PKGBUILDDIR»/test/csq/ENST00000519442/synon-splice-region-del.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000519442/ENST00000519442.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000520795/ENST00000520795.fa -g /«PKGBUILDDIR»/test/csq/ENST00000520795/ENST00000520795.gff /«PKGBUILDDIR»/test/csq/ENST00000520795/long-inside-del.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000520795/ENST00000520795.fa -g /«PKGBUILDDIR»/test/csq/ENST00000520795/ENST00000520795.gff /«PKGBUILDDIR»/test/csq/ENST00000520795/long-inside-del.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000520868/ENST00000520868.fa -g /«PKGBUILDDIR»/test/csq/ENST00000520868/ENST00000520868.gff /«PKGBUILDDIR»/test/csq/ENST00000520868/long-deletion.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000520868/ENST00000520868.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000528237/ENST00000528237.fa -g /«PKGBUILDDIR»/test/csq/ENST00000528237/ENST00000528237.gff /«PKGBUILDDIR»/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000528237/ENST00000528237.gff ...
+Indexed 1 transcripts, 7 exons, 6 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000536784/ENST00000536784.fa -g /«PKGBUILDDIR»/test/csq/ENST00000536784/ENST00000536784.gff /«PKGBUILDDIR»/test/csq/ENST00000536784/not-a-start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000536784/ENST00000536784.fa -g /«PKGBUILDDIR»/test/csq/ENST00000536784/ENST00000536784.gff /«PKGBUILDDIR»/test/csq/ENST00000536784/not-a-start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000542803/ENST00000542803.fa -g /«PKGBUILDDIR»/test/csq/ENST00000542803/ENST00000542803.gff /«PKGBUILDDIR»/test/csq/ENST00000542803/splice-region.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000542803/ENST00000542803.fa -g /«PKGBUILDDIR»/test/csq/ENST00000542803/ENST00000542803.gff /«PKGBUILDDIR»/test/csq/ENST00000542803/splice-region.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000543077/ENST00000543077.fa -g /«PKGBUILDDIR»/test/csq/ENST00000543077/ENST00000543077.gff /«PKGBUILDDIR»/test/csq/ENST00000543077/not-a-start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000543077/ENST00000543077.fa -g /«PKGBUILDDIR»/test/csq/ENST00000543077/ENST00000543077.gff /«PKGBUILDDIR»/test/csq/ENST00000543077/not-a-start-lost.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000545279/ENST00000545279.fa -g /«PKGBUILDDIR»/test/csq/ENST00000545279/ENST00000545279.gff /«PKGBUILDDIR»/test/csq/ENST00000545279/splice-region-insert.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000545279/ENST00000545279.gff ...
+Indexed 1 transcripts, 9 exons, 7 CDSs, 4 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000557788/ENST00000557788.fa -g /«PKGBUILDDIR»/test/csq/ENST00000557788/ENST00000557788.gff /«PKGBUILDDIR»/test/csq/ENST00000557788/long-overlap-del.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000557788/ENST00000557788.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000573314/ENST00000573314.fa -g /«PKGBUILDDIR»/test/csq/ENST00000573314/ENST00000573314.gff /«PKGBUILDDIR»/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -l -f /«PKGBUILDDIR»/test/csq/ENST00000573314/ENST00000573314.fa -g /«PKGBUILDDIR»/test/csq/ENST00000573314/ENST00000573314.gff /«PKGBUILDDIR»/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000593942/ENST00000593942.fa -g /«PKGBUILDDIR»/test/csq/ENST00000593942/ENST00000593942.gff /«PKGBUILDDIR»/test/csq/ENST00000593942/last-codon-deletion.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000593942/ENST00000593942.gff ...
+Indexed 1 transcripts, 7 exons, 4 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /«PKGBUILDDIR»/bcftools csq -f /«PKGBUILDDIR»/test/csq/ENST00000624631/ENST00000624631.fa -g /«PKGBUILDDIR»/test/csq/ENST00000624631/ENST00000624631.gff /«PKGBUILDDIR»/test/csq/ENST00000624631/ambiguous.vcf | /«PKGBUILDDIR»/test/csq/sort-csq | /«PKGBUILDDIR»/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /«PKGBUILDDIR»/test/csq/ENST00000624631/ENST00000624631.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+
+Number of tests:
+ total .. 728
+ passed .. 662
+ failed .. 66
+
+Makefile:246: recipe for target 'test-plugins' failed
+make[1]: *** [test-plugins] Error 1
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+dh_auto_test: make -j2 test VERBOSE=1 returned exit code 2
+debian/rules:7: recipe for target 'build-arch' failed
+make: *** [build-arch] Error 2
+dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20171211-1624
+
+Finished
+────────
+
+E: Build failure (dpkg-buildpackage died)
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Cleanup │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /«BUILDDIR»
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build Architecture: kfreebsd-i386
+Build-Space: 22224
+Build-Time: 82
+Distribution: experimental
+Fail-Stage: build
+Host Architecture: kfreebsd-i386
+Install-Time: 54
+Job: bcftools_1.6-1
+Machine Architecture: kfreebsd-i386
+Package: bcftools
+Package-Time: 173
+Source-Version: 1.6-1
+Space: 22224
+Status: attempted
+Version: 1.6-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20171211-1624
+Build needed 00:02:53, 22224k disc space
diff --git a/bcftools_1.6-1_mips.log b/bcftools_1.6-1_mips.log
new file mode 100644
index 0000000..5eac73e
--- /dev/null
+++ b/bcftools_1.6-1_mips.log
@@ -0,0 +1,4528 @@
+
+sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on mips-aql-02.debian.org
+
++==============================================================================+
+| bcftools 1.6-1 (mips) Mon, 11 Dec 2017 16:54:38 +0000 |
++==============================================================================+
+
+Package: bcftools
+Version: 1.6-1
+Source Version: 1.6-1
+Distribution: experimental
+Machine Architecture: mips
+Host Architecture: mips
+Build Architecture: mips
+Build Type: any
+
+I: NOTICE: Log filtering will replace 'var/run/schroot/mount/experimental-mips-sbuild-f376122f-5dcb-40dc-afde-23b653950746' with '<<CHROOT>>'
+
++------------------------------------------------------------------------------+
+| Update chroot |
++------------------------------------------------------------------------------+
+
+Get:1 http://ftp.uk.debian.org/debian unstable InRelease [240 kB]
+Get:2 http://ftp.uk.debian.org/debian experimental InRelease [107 kB]
+Get:3 http://ftp.debian.org/debian unstable InRelease [240 kB]
+Get:4 http://ftp.debian.org/debian experimental InRelease [107 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:6 http://incoming.debian.org/debian-buildd buildd-experimental InRelease [58.9 kB]
+Get:7 http://ftp.uk.debian.org/debian unstable/non-free Sources [83.9 kB]
+Get:8 http://ftp.uk.debian.org/debian unstable/contrib Sources [50.5 kB]
+Get:9 http://ftp.uk.debian.org/debian unstable/main Sources [7953 kB]
+Get:10 http://ftp.uk.debian.org/debian unstable/contrib mips Packages [45.5 kB]
+Get:11 http://ftp.uk.debian.org/debian unstable/main mips Packages [7517 kB]
+Get:12 http://ftp.uk.debian.org/debian experimental/main Sources [262 kB]
+Get:13 http://ftp.uk.debian.org/debian experimental/non-free Sources [3012 B]
+Get:14 http://ftp.uk.debian.org/debian experimental/contrib Sources [1692 B]
+Get:15 http://ftp.uk.debian.org/debian experimental/contrib mips Packages [1564 B]
+Get:16 http://ftp.uk.debian.org/debian experimental/main mips Packages [383 kB]
+Get:17 http://ftp.debian.org/debian unstable/contrib Sources [50.5 kB]
+Get:18 http://ftp.debian.org/debian unstable/main Sources [7953 kB]
+Get:19 http://ftp.debian.org/debian unstable/non-free Sources [83.9 kB]
+Get:20 http://ftp.debian.org/debian unstable/main mips Packages [7517 kB]
+Get:21 http://ftp.debian.org/debian unstable/contrib mips Packages [45.5 kB]
+Get:22 http://ftp.debian.org/debian experimental/contrib Sources [1692 B]
+Get:23 http://ftp.debian.org/debian experimental/non-free Sources [3012 B]
+Get:24 http://ftp.debian.org/debian experimental/main Sources [262 kB]
+Get:25 http://ftp.debian.org/debian experimental/contrib mips Packages [1564 B]
+Get:26 http://ftp.debian.org/debian experimental/main mips Packages [383 kB]
+Get:27 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1916 B]
+Get:28 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [123 kB]
+Get:29 http://incoming.debian.org/debian-buildd buildd-unstable/contrib mips Packages [2832 B]
+Get:30 http://incoming.debian.org/debian-buildd buildd-unstable/main mips Packages [133 kB]
+Get:31 http://incoming.debian.org/debian-buildd buildd-experimental/main Sources [30.7 kB]
+Get:32 http://incoming.debian.org/debian-buildd buildd-experimental/main mips Packages [61.8 kB]
+Fetched 33.8 MB in 24s (1376 kB/s)
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Fetch source files |
++------------------------------------------------------------------------------+
+
+
+Check APT
+---------
+
+Checking available source versions...
+
+Download source files with APT
+------------------------------
+
+Reading package lists...
+NOTICE: 'bcftools' packaging is maintained in the 'Git' version control system at:
+https://anonscm.debian.org/git/debian-med/bcftools.git
+Please use:
+git clone https://anonscm.debian.org/git/debian-med/bcftools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 2342 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (dsc) [2110 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (tar) [2333 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (diff) [6088 B]
+Fetched 2342 kB in 1s (1567 kB/s)
+Download complete and in download only mode
+I: NOTICE: Log filtering will replace 'build/bcftools-0LeBhf/bcftools-1.6' with '<<PKGBUILDDIR>>'
+I: NOTICE: Log filtering will replace 'build/bcftools-0LeBhf' with '<<BUILDDIR>>'
+
++------------------------------------------------------------------------------+
+| 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 '/<<BUILDDIR>>/resolver-9nHjVn/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:/<<BUILDDIR>>/resolver-9nHjVn/apt_archive ./ InRelease
+Get:2 copy:/<<BUILDDIR>>/resolver-9nHjVn/apt_archive ./ Release [957 B]
+Ign:3 copy:/<<BUILDDIR>>/resolver-9nHjVn/apt_archive ./ Release.gpg
+Get:4 copy:/<<BUILDDIR>>/resolver-9nHjVn/apt_archive ./ Sources [349 B]
+Get:5 copy:/<<BUILDDIR>>/resolver-9nHjVn/apt_archive ./ Packages [432 B]
+Fetched 1738 B in 0s (14.4 kB/s)
+Reading package lists...
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Install core build dependencies (aptitude-based resolver) |
++------------------------------------------------------------------------------+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following additional packages will be installed:
+ aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+Suggested packages:
+ aptitude-doc-en | aptitude-doc apt-xapian-index debtags tasksel
+ libcwidget-dev xapian-tools
+Recommended packages:
+ libparse-debianchangelog-perl
+The following NEW packages will be installed:
+ aptitude aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded.
+Need to get 4894 kB of archives.
+After this operation, 21.4 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian unstable/main mips libxapian30 mips 1.4.5-1 [993 kB]
+Get:2 http://ftp.uk.debian.org/debian unstable/main mips libsqlite3-0 mips 3.21.0-1 [563 kB]
+Get:3 http://ftp.uk.debian.org/debian unstable/main mips aptitude-common all 0.8.10-1 [1591 kB]
+Get:4 http://ftp.uk.debian.org/debian unstable/main mips libboost-system1.62.0 mips 1.62.0+dfsg-4+b2 [32.7 kB]
+Get:5 http://ftp.uk.debian.org/debian unstable/main mips libboost-filesystem1.62.0 mips 1.62.0+dfsg-4+b2 [60.3 kB]
+Get:6 http://ftp.uk.debian.org/debian unstable/main mips libboost-iostreams1.62.0 mips 1.62.0+dfsg-4+b2 [49.7 kB]
+Get:7 http://ftp.uk.debian.org/debian unstable/main mips libsigc++-2.0-0v5 mips 2.10.0-1 [61.0 kB]
+Get:8 http://ftp.uk.debian.org/debian unstable/main mips libcwidget3v5 mips 0.5.17-6 [231 kB]
+Get:9 http://ftp.uk.debian.org/debian unstable/main mips aptitude mips 0.8.10-1 [1312 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 4894 kB in 0s (11.3 MB/s)
+Selecting previously unselected package libxapian30:mips.
+(Reading database ... 11496 files and directories currently installed.)
+Preparing to unpack .../0-libxapian30_1.4.5-1_mips.deb ...
+Unpacking libxapian30:mips (1.4.5-1) ...
+Selecting previously unselected package libsqlite3-0:mips.
+Preparing to unpack .../1-libsqlite3-0_3.21.0-1_mips.deb ...
+Unpacking libsqlite3-0:mips (3.21.0-1) ...
+Selecting previously unselected package aptitude-common.
+Preparing to unpack .../2-aptitude-common_0.8.10-1_all.deb ...
+Unpacking aptitude-common (0.8.10-1) ...
+Selecting previously unselected package libboost-system1.62.0:mips.
+Preparing to unpack .../3-libboost-system1.62.0_1.62.0+dfsg-4+b2_mips.deb ...
+Unpacking libboost-system1.62.0:mips (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libboost-filesystem1.62.0:mips.
+Preparing to unpack .../4-libboost-filesystem1.62.0_1.62.0+dfsg-4+b2_mips.deb ...
+Unpacking libboost-filesystem1.62.0:mips (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libboost-iostreams1.62.0:mips.
+Preparing to unpack .../5-libboost-iostreams1.62.0_1.62.0+dfsg-4+b2_mips.deb ...
+Unpacking libboost-iostreams1.62.0:mips (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libsigc++-2.0-0v5:mips.
+Preparing to unpack .../6-libsigc++-2.0-0v5_2.10.0-1_mips.deb ...
+Unpacking libsigc++-2.0-0v5:mips (2.10.0-1) ...
+Selecting previously unselected package libcwidget3v5:mips.
+Preparing to unpack .../7-libcwidget3v5_0.5.17-6_mips.deb ...
+Unpacking libcwidget3v5:mips (0.5.17-6) ...
+Selecting previously unselected package aptitude.
+Preparing to unpack .../8-aptitude_0.8.10-1_mips.deb ...
+Unpacking aptitude (0.8.10-1) ...
+Setting up libxapian30:mips (1.4.5-1) ...
+Setting up aptitude-common (0.8.10-1) ...
+Setting up libboost-iostreams1.62.0:mips (1.62.0+dfsg-4+b2) ...
+Processing triggers for libc-bin (2.25-3) ...
+Setting up libsqlite3-0:mips (3.21.0-1) ...
+Setting up libsigc++-2.0-0v5:mips (2.10.0-1) ...
+Setting up libboost-system1.62.0:mips (1.62.0+dfsg-4+b2) ...
+Setting up libboost-filesystem1.62.0:mips (1.62.0+dfsg-4+b2) ...
+Setting up libcwidget3v5:mips (0.5.17-6) ...
+Setting up aptitude (0.8.10-1) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode
+Processing triggers for libc-bin (2.25-3) ...
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-core-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-core-dummy:mips
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+0 packages upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
+Need to get 852 B of archives. After unpacking 0 B will be used.
+Writing extended state information...
+Get: 1 copy:/<<BUILDDIR>>/resolver-9nHjVn/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
+Fetched 852 B in 0s (22.6 kB/s)
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11750 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_mips.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+
++------------------------------------------------------------------------------+
+| Check architectures |
++------------------------------------------------------------------------------+
+
+Arch check ok (mips included in any)
+
++------------------------------------------------------------------------------+
+| Install package build dependencies |
++------------------------------------------------------------------------------+
+
+
+Setup apt archive
+-----------------
+
+Merged Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+Filtered Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<<BUILDDIR>>/resolver-9nHjVn/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:/<<BUILDDIR>>/resolver-9nHjVn/apt_archive ./ InRelease
+Get:2 copy:/<<BUILDDIR>>/resolver-9nHjVn/apt_archive ./ Release [963 B]
+Ign:3 copy:/<<BUILDDIR>>/resolver-9nHjVn/apt_archive ./ Release.gpg
+Get:4 copy:/<<BUILDDIR>>/resolver-9nHjVn/apt_archive ./ Sources [546 B]
+Get:5 copy:/<<BUILDDIR>>/resolver-9nHjVn/apt_archive ./ Packages [617 B]
+Fetched 2126 B in 0s (17.6 kB/s)
+Reading package lists...
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Install bcftools build dependencies (aptitude-based resolver) |
++------------------------------------------------------------------------------+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+aptitude is already the newest version (0.8.10-1).
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-bcftools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-bcftool [...]
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libbz2-dev{a} libcroco3{a} libcurl3-gnutls{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu57{a} libio-pty-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} l [...]
+The following packages are RECOMMENDED but will NOT be installed:
+ bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules publicsuffix shared-mime-info wget xdg-user-dirs
+0 packages upgraded, 56 newly installed, 0 to remove and 0 not upgraded.
+Need to get 25.4 MB of archives. After unpacking 90.0 MB will be used.
+Writing extended state information...
+Get: 1 copy:/<<BUILDDIR>>/resolver-9nHjVn/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [904 B]
+Get: 2 http://ftp.uk.debian.org/debian unstable/main mips groff-base mips 1.22.3-9 [1275 kB]
+Get: 3 http://ftp.uk.debian.org/debian unstable/main mips libbsd0 mips 0.8.6-3 [105 kB]
+Get: 4 http://ftp.uk.debian.org/debian unstable/main mips libncurses5 mips 6.0+20171125-1 [80.9 kB]
+Get: 5 http://ftp.uk.debian.org/debian unstable/main mips bsdmainutils mips 9.0.14 [187 kB]
+Get: 6 http://ftp.uk.debian.org/debian unstable/main mips libpipeline1 mips 1.5.0-1 [27.8 kB]
+Get: 7 http://ftp.uk.debian.org/debian unstable/main mips man-db mips 2.7.6.1-4 [1031 kB]
+Get: 8 http://ftp.uk.debian.org/debian unstable/main mips libssl1.1 mips 1.1.0g-2 [986 kB]
+Get: 9 http://incoming.debian.org/debian-buildd buildd-unstable/main mips libhts2 mips 1.5-6 [274 kB]
+Get: 10 http://ftp.uk.debian.org/debian unstable/main mips libmagic-mgc mips 1:5.32-1 [226 kB]
+Get: 11 http://ftp.uk.debian.org/debian unstable/main mips libmagic1 mips 1:5.32-1 [112 kB]
+Get: 12 http://ftp.uk.debian.org/debian unstable/main mips file mips 1:5.32-1 [64.2 kB]
+Get: 13 http://ftp.uk.debian.org/debian unstable/main mips gettext-base mips 0.19.8.1-4 [120 kB]
+Get: 14 http://ftp.uk.debian.org/debian unstable/main mips libkeyutils1 mips 1.5.9-9.2 [12.3 kB]
+Get: 15 http://ftp.uk.debian.org/debian unstable/main mips libkrb5support0 mips 1.15.2-2 [60.5 kB]
+Get: 16 http://ftp.uk.debian.org/debian unstable/main mips libk5crypto3 mips 1.15.2-2 [123 kB]
+Get: 17 http://ftp.uk.debian.org/debian unstable/main mips libkrb5-3 mips 1.15.2-2 [278 kB]
+Get: 18 http://ftp.uk.debian.org/debian unstable/main mips libgssapi-krb5-2 mips 1.15.2-2 [139 kB]
+Get: 19 http://ftp.uk.debian.org/debian unstable/main mips libsasl2-modules-db mips 2.1.27~101-g0780600+dfsg-3 [67.4 kB]
+Get: 20 http://ftp.uk.debian.org/debian unstable/main mips libsasl2-2 mips 2.1.27~101-g0780600+dfsg-3 [99.9 kB]
+Get: 21 http://ftp.uk.debian.org/debian unstable/main mips libldap-common all 2.4.45+dfsg-1 [87.0 kB]
+Get: 22 http://ftp.uk.debian.org/debian unstable/main mips libldap-2.4-2 mips 2.4.45+dfsg-1 [199 kB]
+Get: 23 http://ftp.uk.debian.org/debian unstable/main mips libicu57 mips 57.1-8 [7482 kB]
+Get: 24 http://ftp.uk.debian.org/debian unstable/main mips libxml2 mips 2.9.4+dfsg1-5.1 [626 kB]
+Get: 25 http://ftp.uk.debian.org/debian unstable/main mips libsigsegv2 mips 2.11-1 [29.6 kB]
+Get: 26 http://ftp.uk.debian.org/debian unstable/main mips m4 mips 1.4.18-1 [197 kB]
+Get: 27 http://ftp.uk.debian.org/debian unstable/main mips autoconf all 2.69-11 [341 kB]
+Get: 28 http://ftp.uk.debian.org/debian unstable/main mips autotools-dev all 20161112.1+nmu1 [74.2 kB]
+Get: 29 http://ftp.uk.debian.org/debian unstable/main mips automake all 1:1.15.1-3 [736 kB]
+Get: 30 http://ftp.uk.debian.org/debian unstable/main mips autopoint all 0.19.8.1-4 [434 kB]
+Get: 31 http://ftp.uk.debian.org/debian unstable/main mips libtool all 2.4.6-2 [545 kB]
+Get: 32 http://ftp.uk.debian.org/debian unstable/main mips dh-autoreconf all 15 [16.2 kB]
+Get: 33 http://ftp.uk.debian.org/debian unstable/main mips libarchive-zip-perl all 1.59-1 [95.5 kB]
+Get: 34 http://ftp.uk.debian.org/debian unstable/main mips libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
+Get: 35 http://ftp.uk.debian.org/debian unstable/main mips libtimedate-perl all 2.3000-2 [42.2 kB]
+Get: 36 http://ftp.uk.debian.org/debian unstable/main mips dh-strip-nondeterminism all 0.040-1 [11.8 kB]
+Get: 37 http://ftp.uk.debian.org/debian unstable/main mips libglib2.0-0 mips 2.54.2-1 [2642 kB]
+Get: 38 http://incoming.debian.org/debian-buildd buildd-unstable/main mips tabix mips 1.5-6 [309 kB]
+Get: 39 http://ftp.uk.debian.org/debian unstable/main mips libcroco3 mips 0.6.12-1 [131 kB]
+Get: 40 http://ftp.uk.debian.org/debian unstable/main mips gettext mips 0.19.8.1-4 [1250 kB]
+Get: 41 http://incoming.debian.org/debian-buildd buildd-unstable/main mips libhts-dev mips 1.5-6 [388 kB]
+Get: 42 http://ftp.uk.debian.org/debian unstable/main mips intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get: 43 http://ftp.uk.debian.org/debian unstable/main mips po-debconf all 1.0.20 [247 kB]
+Get: 44 http://ftp.uk.debian.org/debian unstable/main mips debhelper all 10.10.9 [975 kB]
+Get: 45 http://ftp.uk.debian.org/debian unstable/main mips libbz2-dev mips 1.0.6-8.1 [31.4 kB]
+Get: 46 http://ftp.uk.debian.org/debian unstable/main mips libnghttp2-14 mips 1.28.0-1 [78.0 kB]
+Get: 47 http://ftp.uk.debian.org/debian unstable/main mips libpsl5 mips 0.19.1-4 [44.0 kB]
+Get: 48 http://ftp.uk.debian.org/debian unstable/main mips librtmp1 mips 2.4+20151223.gitfa8646d.1-1+b1 [55.1 kB]
+Get: 49 http://ftp.uk.debian.org/debian unstable/main mips libssh2-1 mips 1.8.0-1 [132 kB]
+Get: 50 http://ftp.uk.debian.org/debian unstable/main mips libcurl3-gnutls mips 7.57.0-1 [289 kB]
+Get: 51 http://ftp.uk.debian.org/debian unstable/main mips libgslcblas0 mips 2.4+dfsg-6 [94.1 kB]
+Get: 52 http://ftp.uk.debian.org/debian unstable/main mips libgsl23 mips 2.4+dfsg-6 [799 kB]
+Get: 53 http://ftp.uk.debian.org/debian unstable/main mips libgsl-dev mips 2.4+dfsg-6 [1141 kB]
+Get: 54 http://ftp.uk.debian.org/debian unstable/main mips liblzma-dev mips 5.2.2-1.3 [297 kB]
+Get: 55 http://ftp.uk.debian.org/debian unstable/main mips libio-pty-perl mips 1:1.08-1.1+b4 [31.3 kB]
+Get: 56 http://ftp.uk.debian.org/debian unstable/main mips zlib1g-dev mips 1:1.2.8.dfsg-5 [204 kB]
+Fetched 25.4 MB in 1s (15.4 MB/s)
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package groff-base.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11750 files and directories currently installed.)
+Preparing to unpack .../00-groff-base_1.22.3-9_mips.deb ...
+Unpacking groff-base (1.22.3-9) ...
+Selecting previously unselected package libbsd0:mips.
+Preparing to unpack .../01-libbsd0_0.8.6-3_mips.deb ...
+Unpacking libbsd0:mips (0.8.6-3) ...
+Selecting previously unselected package libncurses5:mips.
+Preparing to unpack .../02-libncurses5_6.0+20171125-1_mips.deb ...
+Unpacking libncurses5:mips (6.0+20171125-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../03-bsdmainutils_9.0.14_mips.deb ...
+Unpacking bsdmainutils (9.0.14) ...
+Selecting previously unselected package libpipeline1:mips.
+Preparing to unpack .../04-libpipeline1_1.5.0-1_mips.deb ...
+Unpacking libpipeline1:mips (1.5.0-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../05-man-db_2.7.6.1-4_mips.deb ...
+Unpacking man-db (2.7.6.1-4) ...
+Selecting previously unselected package libssl1.1:mips.
+Preparing to unpack .../06-libssl1.1_1.1.0g-2_mips.deb ...
+Unpacking libssl1.1:mips (1.1.0g-2) ...
+Selecting previously unselected package libmagic-mgc.
+Preparing to unpack .../07-libmagic-mgc_1%3a5.32-1_mips.deb ...
+Unpacking libmagic-mgc (1:5.32-1) ...
+Selecting previously unselected package libmagic1:mips.
+Preparing to unpack .../08-libmagic1_1%3a5.32-1_mips.deb ...
+Unpacking libmagic1:mips (1:5.32-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../09-file_1%3a5.32-1_mips.deb ...
+Unpacking file (1:5.32-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../10-gettext-base_0.19.8.1-4_mips.deb ...
+Unpacking gettext-base (0.19.8.1-4) ...
+Selecting previously unselected package libkeyutils1:mips.
+Preparing to unpack .../11-libkeyutils1_1.5.9-9.2_mips.deb ...
+Unpacking libkeyutils1:mips (1.5.9-9.2) ...
+Selecting previously unselected package libkrb5support0:mips.
+Preparing to unpack .../12-libkrb5support0_1.15.2-2_mips.deb ...
+Unpacking libkrb5support0:mips (1.15.2-2) ...
+Selecting previously unselected package libk5crypto3:mips.
+Preparing to unpack .../13-libk5crypto3_1.15.2-2_mips.deb ...
+Unpacking libk5crypto3:mips (1.15.2-2) ...
+Selecting previously unselected package libkrb5-3:mips.
+Preparing to unpack .../14-libkrb5-3_1.15.2-2_mips.deb ...
+Unpacking libkrb5-3:mips (1.15.2-2) ...
+Selecting previously unselected package libgssapi-krb5-2:mips.
+Preparing to unpack .../15-libgssapi-krb5-2_1.15.2-2_mips.deb ...
+Unpacking libgssapi-krb5-2:mips (1.15.2-2) ...
+Selecting previously unselected package libsasl2-modules-db:mips.
+Preparing to unpack .../16-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3_mips.deb ...
+Unpacking libsasl2-modules-db:mips (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libsasl2-2:mips.
+Preparing to unpack .../17-libsasl2-2_2.1.27~101-g0780600+dfsg-3_mips.deb ...
+Unpacking libsasl2-2:mips (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libldap-common.
+Preparing to unpack .../18-libldap-common_2.4.45+dfsg-1_all.deb ...
+Unpacking libldap-common (2.4.45+dfsg-1) ...
+Selecting previously unselected package libldap-2.4-2:mips.
+Preparing to unpack .../19-libldap-2.4-2_2.4.45+dfsg-1_mips.deb ...
+Unpacking libldap-2.4-2:mips (2.4.45+dfsg-1) ...
+Selecting previously unselected package libicu57:mips.
+Preparing to unpack .../20-libicu57_57.1-8_mips.deb ...
+Unpacking libicu57:mips (57.1-8) ...
+Selecting previously unselected package libxml2:mips.
+Preparing to unpack .../21-libxml2_2.9.4+dfsg1-5.1_mips.deb ...
+Unpacking libxml2:mips (2.9.4+dfsg1-5.1) ...
+Selecting previously unselected package libsigsegv2:mips.
+Preparing to unpack .../22-libsigsegv2_2.11-1_mips.deb ...
+Unpacking libsigsegv2:mips (2.11-1) ...
+Selecting previously unselected package m4.
+Preparing to unpack .../23-m4_1.4.18-1_mips.deb ...
+Unpacking m4 (1.4.18-1) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../24-autoconf_2.69-11_all.deb ...
+Unpacking autoconf (2.69-11) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../25-autotools-dev_20161112.1+nmu1_all.deb ...
+Unpacking autotools-dev (20161112.1+nmu1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../26-automake_1%3a1.15.1-3_all.deb ...
+Unpacking automake (1:1.15.1-3) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../27-autopoint_0.19.8.1-4_all.deb ...
+Unpacking autopoint (0.19.8.1-4) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../28-libtool_2.4.6-2_all.deb ...
+Unpacking libtool (2.4.6-2) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../29-dh-autoreconf_15_all.deb ...
+Unpacking dh-autoreconf (15) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../30-libarchive-zip-perl_1.59-1_all.deb ...
+Unpacking libarchive-zip-perl (1.59-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../31-libfile-stripnondeterminism-perl_0.040-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.040-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../32-libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../33-dh-strip-nondeterminism_0.040-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.040-1) ...
+Selecting previously unselected package libglib2.0-0:mips.
+Preparing to unpack .../34-libglib2.0-0_2.54.2-1_mips.deb ...
+Unpacking libglib2.0-0:mips (2.54.2-1) ...
+Selecting previously unselected package libcroco3:mips.
+Preparing to unpack .../35-libcroco3_0.6.12-1_mips.deb ...
+Unpacking libcroco3:mips (0.6.12-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../36-gettext_0.19.8.1-4_mips.deb ...
+Unpacking gettext (0.19.8.1-4) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../37-intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../38-po-debconf_1.0.20_all.deb ...
+Unpacking po-debconf (1.0.20) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../39-debhelper_10.10.9_all.deb ...
+Unpacking debhelper (10.10.9) ...
+Selecting previously unselected package libbz2-dev:mips.
+Preparing to unpack .../40-libbz2-dev_1.0.6-8.1_mips.deb ...
+Unpacking libbz2-dev:mips (1.0.6-8.1) ...
+Selecting previously unselected package libnghttp2-14:mips.
+Preparing to unpack .../41-libnghttp2-14_1.28.0-1_mips.deb ...
+Unpacking libnghttp2-14:mips (1.28.0-1) ...
+Selecting previously unselected package libpsl5:mips.
+Preparing to unpack .../42-libpsl5_0.19.1-4_mips.deb ...
+Unpacking libpsl5:mips (0.19.1-4) ...
+Selecting previously unselected package librtmp1:mips.
+Preparing to unpack .../43-librtmp1_2.4+20151223.gitfa8646d.1-1+b1_mips.deb ...
+Unpacking librtmp1:mips (2.4+20151223.gitfa8646d.1-1+b1) ...
+Selecting previously unselected package libssh2-1:mips.
+Preparing to unpack .../44-libssh2-1_1.8.0-1_mips.deb ...
+Unpacking libssh2-1:mips (1.8.0-1) ...
+Selecting previously unselected package libcurl3-gnutls:mips.
+Preparing to unpack .../45-libcurl3-gnutls_7.57.0-1_mips.deb ...
+Unpacking libcurl3-gnutls:mips (7.57.0-1) ...
+Selecting previously unselected package libgslcblas0:mips.
+Preparing to unpack .../46-libgslcblas0_2.4+dfsg-6_mips.deb ...
+Unpacking libgslcblas0:mips (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl23:mips.
+Preparing to unpack .../47-libgsl23_2.4+dfsg-6_mips.deb ...
+Unpacking libgsl23:mips (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl-dev.
+Preparing to unpack .../48-libgsl-dev_2.4+dfsg-6_mips.deb ...
+Unpacking libgsl-dev (2.4+dfsg-6) ...
+Selecting previously unselected package libhts2:mips.
+Preparing to unpack .../49-libhts2_1.5-6_mips.deb ...
+Unpacking libhts2:mips (1.5-6) ...
+Selecting previously unselected package liblzma-dev:mips.
+Preparing to unpack .../50-liblzma-dev_5.2.2-1.3_mips.deb ...
+Unpacking liblzma-dev:mips (5.2.2-1.3) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../51-tabix_1.5-6_mips.deb ...
+Unpacking tabix (1.5-6) ...
+Selecting previously unselected package libhts-dev:mips.
+Preparing to unpack .../52-libhts-dev_1.5-6_mips.deb ...
+Unpacking libhts-dev:mips (1.5-6) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../53-libio-pty-perl_1%3a1.08-1.1+b4_mips.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b4) ...
+Selecting previously unselected package zlib1g-dev:mips.
+Preparing to unpack .../54-zlib1g-dev_1%3a1.2.8.dfsg-5_mips.deb ...
+Unpacking zlib1g-dev:mips (1:1.2.8.dfsg-5) ...
+Selecting previously unselected package sbuild-build-depends-bcftools-dummy.
+Preparing to unpack .../55-sbuild-build-depends-bcftools-dummy_0.invalid.0_mips.deb ...
+Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Setting up libncurses5:mips (6.0+20171125-1) ...
+Setting up libbz2-dev:mips (1.0.6-8.1) ...
+Setting up libarchive-zip-perl (1.59-1) ...
+Setting up libnghttp2-14:mips (1.28.0-1) ...
+Setting up libio-pty-perl (1:1.08-1.1+b4) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libsigsegv2:mips (2.11-1) ...
+Setting up libldap-common (2.4.45+dfsg-1) ...
+Setting up libpsl5:mips (0.19.1-4) ...
+Setting up groff-base (1.22.3-9) ...
+Setting up libglib2.0-0:mips (2.54.2-1) ...
+No schema files found: doing nothing.
+Setting up libsasl2-modules-db:mips (2.1.27~101-g0780600+dfsg-3) ...
+Setting up libsasl2-2:mips (2.1.27~101-g0780600+dfsg-3) ...
+Setting up gettext-base (0.19.8.1-4) ...
+Setting up libpipeline1:mips (1.5.0-1) ...
+Setting up librtmp1:mips (2.4+20151223.gitfa8646d.1-1+b1) ...
+Setting up m4 (1.4.18-1) ...
+Setting up libicu57:mips (57.1-8) ...
+Setting up libbsd0:mips (0.8.6-3) ...
+Setting up libxml2:mips (2.9.4+dfsg1-5.1) ...
+Setting up libmagic-mgc (1:5.32-1) ...
+Setting up libmagic1:mips (1:5.32-1) ...
+Setting up libcroco3:mips (0.6.12-1) ...
+Setting up libssh2-1:mips (1.8.0-1) ...
+Processing triggers for libc-bin (2.25-3) ...
+Setting up autotools-dev (20161112.1+nmu1) ...
+Setting up libldap-2.4-2:mips (2.4.45+dfsg-1) ...
+Setting up libssl1.1:mips (1.1.0g-2) ...
+Setting up liblzma-dev:mips (5.2.2-1.3) ...
+Setting up libkeyutils1:mips (1.5.9-9.2) ...
+Setting up bsdmainutils (9.0.14) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libgslcblas0:mips (2.4+dfsg-6) ...
+Setting up autopoint (0.19.8.1-4) ...
+Setting up zlib1g-dev:mips (1:1.2.8.dfsg-5) ...
+Setting up libfile-stripnondeterminism-perl (0.040-1) ...
+Setting up libgsl23:mips (2.4+dfsg-6) ...
+Setting up gettext (0.19.8.1-4) ...
+Setting up libgsl-dev (2.4+dfsg-6) ...
+Setting up autoconf (2.69-11) ...
+Setting up file (1:5.32-1) ...
+Setting up libkrb5support0:mips (1.15.2-2) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up automake (1:1.15.1-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
+Setting up man-db (2.7.6.1-4) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libtool (2.4.6-2) ...
+Setting up libk5crypto3:mips (1.15.2-2) ...
+Setting up po-debconf (1.0.20) ...
+Setting up libkrb5-3:mips (1.15.2-2) ...
+Setting up libgssapi-krb5-2:mips (1.15.2-2) ...
+Setting up libcurl3-gnutls:mips (7.57.0-1) ...
+Setting up tabix (1.5-6) ...
+Setting up libhts2:mips (1.5-6) ...
+Setting up libhts-dev:mips (1.5-6) ...
+Setting up dh-autoreconf (15) ...
+Setting up dh-strip-nondeterminism (0.040-1) ...
+Setting up debhelper (10.10.9) ...
+Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.25-3) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+
++------------------------------------------------------------------------------+
+| Build environment |
++------------------------------------------------------------------------------+
+
+Kernel: Linux 4.9.0-4-octeon mips (mips64)
+Toolchain package versions: binutils_2.29.1-11 dpkg-dev_1.19.0.4 g++-7_7.2.0-17 gcc-7_7.2.0-17 libc6-dev_2.25-3 libstdc++-7-dev_7.2.0-17 libstdc++6_7.2.0-17 linux-libc-dev_4.14.2-1
+Package versions: adduser_3.116 apt_1.6~alpha5 aptitude_0.8.10-1 aptitude-common_0.8.10-1 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-11 binutils-common_2.29.1-11 binutils-mips-linux-gnu_2.29.1-11 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 coreutils_8.28-1 cpp_4:7.2.0-1d1 cpp-7_7.2.0-17 dash_0.5.8-2.5 debconf_1.5.65 debhelper_10.10.9 debian-archive-k [...]
+
++------------------------------------------------------------------------------+
+| Build |
++------------------------------------------------------------------------------+
+
+
+Unpack source
+-------------
+
+gpgv: unknown type of key resource 'trustedkeys.kbx'
+gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
+gpgv: Signature made Mon Dec 11 14:53:09 2017 UTC
+gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
+gpgv: issuer "tillea at rki.de"
+gpgv: Can't check signature: No public key
+dpkg-source: warning: failed to verify signature on ./bcftools_1.6-1.dsc
+dpkg-source: info: extracting bcftools in /<<PKGBUILDDIR>>
+dpkg-source: info: unpacking bcftools_1.6.orig.tar.gz
+dpkg-source: info: unpacking bcftools_1.6-1.debian.tar.xz
+dpkg-source: info: applying tests-pluginpath.patch
+dpkg-source: info: applying test-regidx-unsigned-char.patch
+dpkg-source: info: applying fix-test_vcf_query.patch
+
+Check disk space
+----------------
+
+Sufficient free space for build
+
+User Environment
+----------------
+
+APT_CONFIG=/var/lib/sbuild/apt.conf
+DEB_BUILD_OPTIONS=parallel=2
+HOME=/sbuild-nonexistent
+LC_ALL=POSIX
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=experimental-mips-sbuild
+SCHROOT_CHROOT_NAME=experimental-mips-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1009
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=experimental-mips-sbuild-f376122f-5dcb-40dc-afde-23b653950746
+SCHROOT_UID=2952
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
+XDG_RUNTIME_DIR=/run/user/2952
+XDG_SESSION_ID=c2637
+
+dpkg-buildpackage
+-----------------
+
+dpkg-buildpackage: info: source package bcftools
+dpkg-buildpackage: info: source version 1.6-1
+dpkg-buildpackage: info: source distribution experimental
+ dpkg-source --before-build bcftools-1.6
+dpkg-buildpackage: info: host architecture mips
+ fakeroot debian/rules clean
+rm -f config.mk && touch config.mk
+dh clean --parallel
+ dh_auto_clean
+ make -j2 distclean
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+rm -f test/*.o test/*~
+rm -f plugins/*.so plugins/*.P
+rm -rf plugins/*.dSYM
+rm -f gmon.out *.o *~ version.h plugins/*.so plugins/*.P
+rm -rf *.dSYM plugins/*.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 '/<<PKGBUILDDIR>>'
+ dh_clean
+ debian/rules build-arch
+dh build-arch --parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_autoreconf
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+rm -f config.mk && touch config.mk
+export MAKEFLAGS="-s"; dh_autoreconf
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+dh_auto_configure -- \
+--with-htslib=system \
+--enable-gsl \
+--with-cblas=gslcblas \
+--with-bcf-plugin-dir=/usr/lib/mips-linux-gnu/bcftools
+ ./configure --build=mips-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/mips-linux-gnu --libexecdir=\${prefix}/lib/mips-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/mips-linux-gnu/bcftools
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for 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... -ldl
+checking if the compiler accepts -rdynamic... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ dh_auto_build -a -O--parallel
+ make -j2
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+echo '#define BCFTOOLS_VERSION "1.6"' > version.h
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/mips-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c
+gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl
+gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -ldl -ldl
+gcc -rdynamic -pthread -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 vcfplugin.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 ccall.o em.o prob1.o kmin.o -l [...]
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ dh_auto_test -a -O--parallel
+ make -j2 test VERBOSE=1
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+./test/test-rbuf
+Inserted 1-9 starting at offset 5:
+ 5 6 7 8 9 0 1 2 3
+ 1 2 3 4 5 6 7 8 9
+4th is 4
+Deleting 1-2:
+ 7 8 9 0 1 2 3
+ 3 4 5 6 7 8 9
+Prepending 0-8:
+ 8 9 0 1 2 3 4 5 6 7
+ 8 7 6 5 4 3 2 1 0 3
+Expanding:
+ 8 9 10 11 12 13 14 15 16 17
+ 8 7 6 5 4 3 2 1 0 3
+./test/test-regidx
+REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix=
+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/lWgqPPj34J/merge.a.vcf.gz 2:3199812-3199812
+.. ok
+
+test_tabix:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/lWgqPPj34J/merge.a.bcf 2:3199812-3199812
+.. ok
+
+test_tabix:
+ tabix /tmp/lWgqPPj34J/merge.a.vcf.gz 1:3000151-3000151
+.. ok
+
+test_tabix:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/lWgqPPj34J/merge.a.bcf 1:3000151-3000151
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/lWgqPPj34J/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/lWgqPPj34J/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/lWgqPPj34J/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/lWgqPPj34J/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/lWgqPPj34J/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/lWgqPPj34J/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/lWgqPPj34J/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/lWgqPPj34J/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/lWgqPPj34J/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/lWgqPPj34J/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/lWgqPPj34J/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/lWgqPPj34J/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/lWgqPPj34J/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/lWgqPPj34J/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/lWgqPPj34J/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/lWgqPPj34J/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/lWgqPPj34J/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/lWgqPPj34J/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/lWgqPPj34J/empty.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/lWgqPPj34J/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/lWgqPPj34J/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/lWgqPPj34J/empty.bcf
+.. ok
+
+test_vcf_check:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/lWgqPPj34J/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check_merge:
+ /<<PKGBUILDDIR>>/misc/plot-vcfstats -m /tmp/lWgqPPj34J/check.1.chk /tmp/lWgqPPj34J/check.2.chk /tmp/lWgqPPj34J/check.3.chk /tmp/lWgqPPj34J/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/lWgqPPj34J/stats.a.vcf.gz /tmp/lWgqPPj34J/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s B /tmp/lWgqPPj34J/stats.a.vcf.gz /tmp/lWgqPPj34J/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/lWgqPPj34J/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 /tmp/lWgqPPj34J/isec.a.vcf.gz /tmp/lWgqPPj34J/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 /tmp/lWgqPPj34J/isec.a.vcf.gz /tmp/lWgqPPj34J/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/lWgqPPj34J/isec.a.vcf.gz /tmp/lWgqPPj34J/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/lWgqPPj34J/isec.a.vcf.gz /tmp/lWgqPPj34J/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -c both /tmp/lWgqPPj34J/isec.a.vcf.gz /tmp/lWgqPPj34J/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -c both /tmp/lWgqPPj34J/isec.a.vcf.gz /tmp/lWgqPPj34J/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -c any /tmp/lWgqPPj34J/isec.a.vcf.gz /tmp/lWgqPPj34J/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -c any /tmp/lWgqPPj34J/isec.a.vcf.gz /tmp/lWgqPPj34J/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -C -c any /tmp/lWgqPPj34J/isec.a.vcf.gz /tmp/lWgqPPj34J/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -C -c any /tmp/lWgqPPj34J/isec.a.vcf.gz /tmp/lWgqPPj34J/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec2:
+ /<<PKGBUILDDIR>>/bcftools isec --no-version -T /tmp/lWgqPPj34J/isec.tab.gz /tmp/lWgqPPj34J/isec.a.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/isec.tab.out
+ /<<PKGBUILDDIR>>/test/isec.tab.out.new
+.. failed ...
+
+test_vcf_isec2:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -T /tmp/lWgqPPj34J/isec.tab.gz /tmp/lWgqPPj34J/isec.a.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/isec.tab.out
+ /<<PKGBUILDDIR>>/test/isec.tab.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples /tmp/lWgqPPj34J/merge.a.vcf.gz /tmp/lWgqPPj34J/merge.b.vcf.gz /tmp/lWgqPPj34J/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.out
+ /<<PKGBUILDDIR>>/test/merge.abc.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples /tmp/lWgqPPj34J/merge.a.vcf.gz /tmp/lWgqPPj34J/merge.b.vcf.gz /tmp/lWgqPPj34J/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.out
+ /<<PKGBUILDDIR>>/test/merge.abc.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -Fx /tmp/lWgqPPj34J/merge.a.vcf.gz /tmp/lWgqPPj34J/merge.b.vcf.gz /tmp/lWgqPPj34J/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -Fx /tmp/lWgqPPj34J/merge.a.vcf.gz /tmp/lWgqPPj34J/merge.b.vcf.gz /tmp/lWgqPPj34J/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -0 /tmp/lWgqPPj34J/merge.a.vcf.gz /tmp/lWgqPPj34J/merge.b.vcf.gz /tmp/lWgqPPj34J/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -0 /tmp/lWgqPPj34J/merge.a.vcf.gz /tmp/lWgqPPj34J/merge.b.vcf.gz /tmp/lWgqPPj34J/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m none /tmp/lWgqPPj34J/merge.2.a.vcf.gz /tmp/lWgqPPj34J/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.none.out
+ /<<PKGBUILDDIR>>/test/merge.2.none.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m none /tmp/lWgqPPj34J/merge.2.a.vcf.gz /tmp/lWgqPPj34J/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.none.out
+ /<<PKGBUILDDIR>>/test/merge.2.none.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m both /tmp/lWgqPPj34J/merge.2.a.vcf.gz /tmp/lWgqPPj34J/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.both.out
+ /<<PKGBUILDDIR>>/test/merge.2.both.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m both /tmp/lWgqPPj34J/merge.2.a.vcf.gz /tmp/lWgqPPj34J/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.both.out
+ /<<PKGBUILDDIR>>/test/merge.2.both.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m all /tmp/lWgqPPj34J/merge.2.a.vcf.gz /tmp/lWgqPPj34J/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.all.out
+ /<<PKGBUILDDIR>>/test/merge.2.all.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m all /tmp/lWgqPPj34J/merge.2.a.vcf.gz /tmp/lWgqPPj34J/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.all.out
+ /<<PKGBUILDDIR>>/test/merge.2.all.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/lWgqPPj34J/merge.3.a.vcf.gz /tmp/lWgqPPj34J/merge.3.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.3.out
+ /<<PKGBUILDDIR>>/test/merge.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/lWgqPPj34J/merge.3.a.vcf.gz /tmp/lWgqPPj34J/merge.3.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.3.out
+ /<<PKGBUILDDIR>>/test/merge.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m id /tmp/lWgqPPj34J/merge.4.a.vcf.gz /tmp/lWgqPPj34J/merge.4.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.4.out
+ /<<PKGBUILDDIR>>/test/merge.4.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m id /tmp/lWgqPPj34J/merge.4.a.vcf.gz /tmp/lWgqPPj34J/merge.4.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.4.out
+ /<<PKGBUILDDIR>>/test/merge.4.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - /tmp/lWgqPPj34J/gvcf.merge.1.vcf.gz /tmp/lWgqPPj34J/gvcf.merge.2.vcf.gz /tmp/lWgqPPj34J/gvcf.merge.3.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - /tmp/lWgqPPj34J/gvcf.merge.1.vcf.gz /tmp/lWgqPPj34J/gvcf.merge.2.vcf.gz /tmp/lWgqPPj34J/gvcf.merge.3.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - /tmp/lWgqPPj34J/merge.gvcf.2.a.vcf.gz /tmp/lWgqPPj34J/merge.gvcf.2.b.vcf.gz /tmp/lWgqPPj34J/merge.gvcf.2.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - /tmp/lWgqPPj34J/merge.gvcf.2.a.vcf.gz /tmp/lWgqPPj34J/merge.gvcf.2.b.vcf.gz /tmp/lWgqPPj34J/merge.gvcf.2.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - -i SRC:join /tmp/lWgqPPj34J/merge.gvcf.3.a.vcf.gz /tmp/lWgqPPj34J/merge.gvcf.3.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/lWgqPPj34J/merge.gvcf.3.a.vcf.gz /tmp/lWgqPPj34J/merge.gvcf.3.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version /tmp/lWgqPPj34J/merge.5.a.vcf.gz /tmp/lWgqPPj34J/merge.5.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob /tmp/lWgqPPj34J/merge.5.a.vcf.gz /tmp/lWgqPPj34J/merge.5.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/lWgqPPj34J/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XRI\n' -i'XRI[*]>1111'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' /tmp/lWgqPPj34J/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/lWgqPPj34J/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/lWgqPPj34J/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10' /tmp/lWgqPPj34J/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/lWgqPPj34J/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/lWgqPPj34J/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/lWgqPPj34J/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/lWgqPPj34J/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/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/lWgqPPj34J/view.vectors.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/query.12.out
+ /<<PKGBUILDDIR>>/test/query.12.out.new
+.. failed ...
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/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'
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/query.12.out
+ /<<PKGBUILDDIR>>/test/query.12.out.new
+.. failed ...
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' /tmp/lWgqPPj34J/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' /tmp/lWgqPPj34J/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' /tmp/lWgqPPj34J/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' /tmp/lWgqPPj34J/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/lWgqPPj34J/query.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%LINE' /tmp/lWgqPPj34J/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%LINE'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/lWgqPPj34J/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/lWgqPPj34J/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/lWgqPPj34J/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/lWgqPPj34J/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/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/lWgqPPj34J/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/filter-missing-floats.vcf.gz | /<<PKGBUILDDIR>>/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:
+ /<<PKGBUILDDIR>>/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/lWgqPPj34J/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/filter-missing-floats.vcf.gz | /<<PKGBUILDDIR>>/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:
+ /<<PKGBUILDDIR>>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/lWgqPPj34J/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/lWgqPPj34J/query.filter.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/query.filter.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5'
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -cx -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/lWgqPPj34J/norm.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.out
+ /<<PKGBUILDDIR>>/test/norm.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -cx -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/lWgqPPj34J/norm.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.out
+ /<<PKGBUILDDIR>>/test/norm.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- /tmp/lWgqPPj34J/norm.split.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.split.out
+ /<<PKGBUILDDIR>>/test/norm.split.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- /tmp/lWgqPPj34J/norm.split.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.split.out
+ /<<PKGBUILDDIR>>/test/norm.split.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- /tmp/lWgqPPj34J/norm.split.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- /tmp/lWgqPPj34J/norm.split.2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/lWgqPPj34J/norm.split.vcf.gz 2>/dev/null
+
+ Non-zero status 255
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/lWgqPPj34J/norm.split.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/lWgqPPj34J/norm.merge.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.out
+ /<<PKGBUILDDIR>>/test/norm.merge.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/lWgqPPj34J/norm.merge.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.out
+ /<<PKGBUILDDIR>>/test/norm.merge.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/lWgqPPj34J/norm.merge.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/lWgqPPj34J/norm.merge.2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/lWgqPPj34J/norm.merge.3.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/lWgqPPj34J/norm.merge.3.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.'
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ -s /tmp/lWgqPPj34J/norm.merge.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ -s /tmp/lWgqPPj34J/norm.merge.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -Nc s -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/lWgqPPj34J/norm.setref.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -Nc s -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/lWgqPPj34J/norm.setref.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/lWgqPPj34J/norm.telomere.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/lWgqPPj34J/norm.telomere.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/lWgqPPj34J/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.1.out
+ /<<PKGBUILDDIR>>/test/view.1.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/lWgqPPj34J/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.1.out
+ /<<PKGBUILDDIR>>/test/view.1.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/lWgqPPj34J/view.vcf.gz -r20,Y
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.2.out
+ /<<PKGBUILDDIR>>/test/view.2.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/lWgqPPj34J/view.vcf.gz -r20,Y | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.2.out
+ /<<PKGBUILDDIR>>/test/view.2.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -xs NA00003 /tmp/lWgqPPj34J/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.3.out
+ /<<PKGBUILDDIR>>/test/view.3.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -xs NA00003 /tmp/lWgqPPj34J/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.3.out
+ /<<PKGBUILDDIR>>/test/view.3.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/lWgqPPj34J/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.4.out
+ /<<PKGBUILDDIR>>/test/view.4.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/lWgqPPj34J/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.4.out
+ /<<PKGBUILDDIR>>/test/view.4.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -p /tmp/lWgqPPj34J/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.5.out
+ /<<PKGBUILDDIR>>/test/view.5.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -p /tmp/lWgqPPj34J/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.5.out
+ /<<PKGBUILDDIR>>/test/view.5.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -P /tmp/lWgqPPj34J/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.6.out
+ /<<PKGBUILDDIR>>/test/view.6.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -P /tmp/lWgqPPj34J/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.6.out
+ /<<PKGBUILDDIR>>/test/view.6.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/lWgqPPj34J/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/lWgqPPj34J/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -Hu /tmp/lWgqPPj34J/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -GVsnps /tmp/lWgqPPj34J/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.9.out
+ /<<PKGBUILDDIR>>/test/view.9.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -GVsnps /tmp/lWgqPPj34J/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.9.out
+ /<<PKGBUILDDIR>>/test/view.9.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/lWgqPPj34J/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.10.out
+ /<<PKGBUILDDIR>>/test/view.10.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/lWgqPPj34J/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.10.out
+ /<<PKGBUILDDIR>>/test/view.10.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -s ^NA00003 /tmp/lWgqPPj34J/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.exclude.out
+ /<<PKGBUILDDIR>>/test/view.exclude.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -s ^NA00003 /tmp/lWgqPPj34J/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.exclude.out
+ /<<PKGBUILDDIR>>/test/view.exclude.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version /tmp/lWgqPPj34J/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/view.omitgenotypes.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -G /tmp/lWgqPPj34J/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -G /tmp/lWgqPPj34J/view.omitgenotypes.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -HG /tmp/lWgqPPj34J/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -a /tmp/lWgqPPj34J/many.alleles.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -a /tmp/lWgqPPj34J/many.alleles.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asA /tmp/lWgqPPj34J/view.vectors.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asA /tmp/lWgqPPj34J/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asB /tmp/lWgqPPj34J/view.vectors.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asB /tmp/lWgqPPj34J/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asA /tmp/lWgqPPj34J/view.vectors.2.vcf.gz
+[E::bcf_remove_allele_set] Unexpected number of values in INFO/IAF at 1:10; expected Number=A=2, but found 1
+Error: Could not trim alleles at 1:10
+
+ Non-zero status 255
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asA /tmp/lWgqPPj34J/view.vectors.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_remove_allele_set] Unexpected number of values in INFO/IAF at 1:10; expected Number=A=2, but found 1
+Error: Could not trim alleles at 1:10
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[0]="AAAAAA"' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[2]="C"' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[4]="EE"' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FRS[1]="BB"' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'TXT0="text"' /tmp/lWgqPPj34J/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -T /<<PKGBUILDDIR>>/test/view.chrs.tab /tmp/lWgqPPj34J/view.chrs.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -T /<<PKGBUILDDIR>>/test/view.chrs.tab /tmp/lWgqPPj34J/view.chrs.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -i 'POS>=3062917' /tmp/lWgqPPj34J/filter.2.vcf.gz 1:3062917-3157410
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -i 'POS>=3062917' /tmp/lWgqPPj34J/filter.2.vcf.gz 1:3062917-3157410 | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'TXT0="text"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'TXT0="text"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FRS[1]="BB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FRS[1]="BB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[0]="AAAAAA"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[0]="AAAAAA"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[1]="BBB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[1]="BBB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[4]="EE"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[4]="EE"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/STR="XX"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/STR="XX"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -C5:nonmajor /tmp/lWgqPPj34J/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -c6:nonmajor /tmp/lWgqPPj34J/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -q0.3:major /tmp/lWgqPPj34J/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/lWgqPPj34J/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/lWgqPPj34J/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/lWgqPPj34J/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mg0 /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup.2.out
+ /<<PKGBUILDDIR>>/test/mpileup.2.out.new
+.. failed ...
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mg0 /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup.2.out
+ /<<PKGBUILDDIR>>/test/mpileup.2.out.new
+.. failed ...
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call_cAls:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mA -C alleles -T /tmp/lWgqPPj34J/mpileup.tab.gz /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call_cAls:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mA -C alleles -T /tmp/lWgqPPj34J/mpileup.tab.gz /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv /<<PKGBUILDDIR>>/test/mpileup.c.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv /<<PKGBUILDDIR>>/test/mpileup.c.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -mx -g2 -G2 /<<PKGBUILDDIR>>/test/filter.1.vcf | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/filter.1.out
+ /<<PKGBUILDDIR>>/test/filter.1.out.new
+.. failed ...
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -mx -g2 -G2 /<<PKGBUILDDIR>>/test/filter.1.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/filter.1.out
+ /<<PKGBUILDDIR>>/test/filter.1.out.new
+.. failed ...
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<<PKGBUILDDIR>>/test/filter.2.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'ALT="."' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'ALT="."' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S . -i 'FORMAT/TEST3<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S . -i 'FORMAT/TEST4<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="A"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="A"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="RR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="RR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="RA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="RA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="AR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="AR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="AA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="AA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="aA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="aA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="Aa"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="Aa"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HOM"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HOM"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HET"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HET"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HAP"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HAP"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -m 0 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.zIK4eN
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -Ob -m 0 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.CTgdCQ
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -m 1000 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.Ysmw11
+Merging 3 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -Ob -m 1000 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.TjyCe7
+Merging 3 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<<PKGBUILDDIR>>/test/regions.tab /tmp/lWgqPPj34J/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<<PKGBUILDDIR>>/test/regions.tab
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /<<PKGBUILDDIR>>/test/regions.tab /tmp/lWgqPPj34J/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/lWgqPPj34J/regions.tab.gz /tmp/lWgqPPj34J/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/lWgqPPj34J/regions.tab.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/lWgqPPj34J/regions.tab.gz /tmp/lWgqPPj34J/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/lWgqPPj34J/regions.bed /tmp/lWgqPPj34J/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/lWgqPPj34J/regions.bed
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/lWgqPPj34J/regions.bed /tmp/lWgqPPj34J/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/lWgqPPj34J/regions.bed.gz /tmp/lWgqPPj34J/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/lWgqPPj34J/regions.bed.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/lWgqPPj34J/regions.bed.gz /tmp/lWgqPPj34J/regions.vcf.gz
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/lWgqPPj34J/annotate.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/lWgqPPj34J/annotate.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/lWgqPPj34J/annotate2.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/lWgqPPj34J/annotate2.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/lWgqPPj34J/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/lWgqPPj34J/annotate.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/lWgqPPj34J/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/lWgqPPj34J/annotate.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/lWgqPPj34J/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/lWgqPPj34J/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/lWgqPPj34J/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/lWgqPPj34J/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/lWgqPPj34J/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/lWgqPPj34J/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/lWgqPPj34J/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/lWgqPPj34J/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -x FORMAT /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -x FORMAT /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/lWgqPPj34J/annots4.vcf.gz -c +INFO /tmp/lWgqPPj34J/annotate4.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/lWgqPPj34J/annots4.vcf.gz -c +INFO /tmp/lWgqPPj34J/annotate4.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/lWgqPPj34J/annots4.tab.gz -h /<<PKGBUILDDIR>>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<<PKGBUILDDIR>>/test/annotate4.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/lWgqPPj34J/annots4.tab.gz -h /<<PKGBUILDDIR>>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<<PKGBUILDDIR>>/test/annotate4.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/lWgqPPj34J/annots10.tab.gz -h /<<PKGBUILDDIR>>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<<PKGBUILDDIR>>/test/annotate10.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/lWgqPPj34J/annots10.tab.gz -h /<<PKGBUILDDIR>>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<<PKGBUILDDIR>>/test/annotate10.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/lWgqPPj34J/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/lWgqPPj34J/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/lWgqPPj34J/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/lWgqPPj34J/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/lWgqPPj34J/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<<PKGBUILDDIR>>/test/annotate2.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/lWgqPPj34J/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<<PKGBUILDDIR>>/test/annotate2.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/lWgqPPj34J/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/lWgqPPj34J/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/lWgqPPj34J/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/lWgqPPj34J/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/lWgqPPj34J/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/lWgqPPj34J/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/lWgqPPj34J/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/lWgqPPj34J/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +missing2ref --no-version /tmp/lWgqPPj34J/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +missing2ref --no-version /tmp/lWgqPPj34J/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/lWgqPPj34J/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/lWgqPPj34J/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/lWgqPPj34J/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/lWgqPPj34J/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/lWgqPPj34J/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<<PKGBUILDDIR>>/test/annotate9.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/lWgqPPj34J/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<<PKGBUILDDIR>>/test/annotate9.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-AN-AC --no-version /tmp/lWgqPPj34J/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-AN-AC --no-version /tmp/lWgqPPj34J/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +dosage /tmp/lWgqPPj34J/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +dosage /tmp/lWgqPPj34J/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixploidy --no-version /tmp/lWgqPPj34J/fixploidy.vcf.gz -- -s /<<PKGBUILDDIR>>/test/fixploidy.samples -p /<<PKGBUILDDIR>>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixploidy --no-version /tmp/lWgqPPj34J/fixploidy.bcf -- -s /<<PKGBUILDDIR>>/test/fixploidy.samples -p /<<PKGBUILDDIR>>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/lWgqPPj34J/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/lWgqPPj34J/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/lWgqPPj34J/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/lWgqPPj34J/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/lWgqPPj34J/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/lWgqPPj34J/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/lWgqPPj34J/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/lWgqPPj34J/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/lWgqPPj34J/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/lWgqPPj34J/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/lWgqPPj34J/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/lWgqPPj34J/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/lWgqPPj34J/view.vcf.gz -- -t AC -S /<<PKGBUILDDIR>>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/lWgqPPj34J/view.bcf -- -t AC -S /<<PKGBUILDDIR>>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/lWgqPPj34J/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/lWgqPPj34J/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/lWgqPPj34J/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/lWgqPPj34J/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/lWgqPPj34J/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +trio-switch-rate /tmp/lWgqPPj34J/trio.vcf.gz -- -p /<<PKGBUILDDIR>>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +trio-switch-rate /tmp/lWgqPPj34J/trio.bcf -- -p /<<PKGBUILDDIR>>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +ad-bias /tmp/lWgqPPj34J/ad-bias.vcf.gz -- -s /<<PKGBUILDDIR>>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +ad-bias /tmp/lWgqPPj34J/ad-bias.bcf -- -s /<<PKGBUILDDIR>>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +af-dist /tmp/lWgqPPj34J/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +af-dist /tmp/lWgqPPj34J/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixref /tmp/lWgqPPj34J/fixref.2a.vcf.gz -- -f /<<PKGBUILDDIR>>/test/norm.fa -i /tmp/lWgqPPj34J/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixref /tmp/lWgqPPj34J/fixref.2a.bcf -- -f /<<PKGBUILDDIR>>/test/norm.fa -i /tmp/lWgqPPj34J/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/lWgqPPj34J/aa.vcf.gz -- -f /<<PKGBUILDDIR>>/test/aa.fa -c AA -h /<<PKGBUILDDIR>>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/aa.out
+ /<<PKGBUILDDIR>>/test/aa.out.new
+.. failed ...
+
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/lWgqPPj34J/aa.bcf -- -f /<<PKGBUILDDIR>>/test/aa.fa -c AA -h /<<PKGBUILDDIR>>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/aa.out
+ /<<PKGBUILDDIR>>/test/aa.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/lWgqPPj34J/ref.vcf.gz -- -f /<<PKGBUILDDIR>>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+
+ Non-zero status 1
+.. failed ...
+
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/lWgqPPj34J/ref.bcf -- -f /<<PKGBUILDDIR>>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/ref.out
+ /<<PKGBUILDDIR>>/test/ref.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/lWgqPPj34J/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/lWgqPPj34J/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/lWgqPPj34J/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/lWgqPPj34J/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/lWgqPPj34J/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/lWgqPPj34J/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/lWgqPPj34J/mendelian.vcf.gz -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/lWgqPPj34J/mendelian.bcf -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/lWgqPPj34J/mendelian.vcf.gz -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/lWgqPPj34J/mendelian.bcf -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/lWgqPPj34J/mendelian.vcf.gz -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/lWgqPPj34J/mendelian.bcf -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version /tmp/lWgqPPj34J/concat.1.a.vcf.gz /tmp/lWgqPPj34J/concat.1.b.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob /tmp/lWgqPPj34J/concat.1.a.vcf.gz /tmp/lWgqPPj34J/concat.1.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.1.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.1.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version /tmp/lWgqPPj34J/concat.1.a.bcf /tmp/lWgqPPj34J/concat.1.b.bcf
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob /tmp/lWgqPPj34J/concat.1.a.bcf /tmp/lWgqPPj34J/concat.1.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -a /tmp/lWgqPPj34J/concat.2.a.vcf.gz /tmp/lWgqPPj34J/concat.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -a /tmp/lWgqPPj34J/concat.2.a.vcf.gz /tmp/lWgqPPj34J/concat.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -a /tmp/lWgqPPj34J/concat.2.a.bcf /tmp/lWgqPPj34J/concat.2.b.bcf
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -a /tmp/lWgqPPj34J/concat.2.a.bcf /tmp/lWgqPPj34J/concat.2.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -aD /tmp/lWgqPPj34J/concat.2.a.vcf.gz /tmp/lWgqPPj34J/concat.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -aD /tmp/lWgqPPj34J/concat.2.a.vcf.gz /tmp/lWgqPPj34J/concat.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -aD /tmp/lWgqPPj34J/concat.2.a.bcf /tmp/lWgqPPj34J/concat.2.b.bcf
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -aD /tmp/lWgqPPj34J/concat.2.a.bcf /tmp/lWgqPPj34J/concat.2.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -l /tmp/lWgqPPj34J/concat.3.a.vcf.gz /tmp/lWgqPPj34J/concat.3.b.vcf.gz /tmp/lWgqPPj34J/concat.3.0.vcf.gz /tmp/lWgqPPj34J/concat.3.c.vcf.gz /tmp/lWgqPPj34J/concat.3.d.vcf.gz /tmp/lWgqPPj34J/concat.3.e.vcf.gz /tmp/lWgqPPj34J/concat.3.f.vcf.gz
+[E::vcf_format] Invalid BCF, the FORMAT tag id=-13056 not present in the header
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -l /tmp/lWgqPPj34J/concat.3.a.vcf.gz /tmp/lWgqPPj34J/concat.3.b.vcf.gz /tmp/lWgqPPj34J/concat.3.0.vcf.gz /tmp/lWgqPPj34J/concat.3.c.vcf.gz /tmp/lWgqPPj34J/concat.3.d.vcf.gz /tmp/lWgqPPj34J/concat.3.e.vcf.gz /tmp/lWgqPPj34J/concat.3.f.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+GT is not present at 2:280. (This warning is printed only once.)
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -13056
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out.new
+.. failed ...
+
+[W::bcf_record_check] Bad BCF record: Invalid INFO id -14336
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -l /tmp/lWgqPPj34J/concat.3.a.bcf /tmp/lWgqPPj34J/concat.3.b.bcf /tmp/lWgqPPj34J/concat.3.0.bcf /tmp/lWgqPPj34J/concat.3.c.bcf /tmp/lWgqPPj34J/concat.3.d.bcf /tmp/lWgqPPj34J/concat.3.e.bcf /tmp/lWgqPPj34J/concat.3.f.bcf
+[W::bcf_record_check] Bad BCF record: Invalid INFO id -14336
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080
+[E::vcf_format] Invalid BCF, the FORMAT tag id=-13056 not present in the header
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -l /tmp/lWgqPPj34J/concat.3.a.bcf /tmp/lWgqPPj34J/concat.3.b.bcf /tmp/lWgqPPj34J/concat.3.0.bcf /tmp/lWgqPPj34J/concat.3.c.bcf /tmp/lWgqPPj34J/concat.3.d.bcf /tmp/lWgqPPj34J/concat.3.e.bcf /tmp/lWgqPPj34J/concat.3.f.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[W::bcf_record_check] Bad BCF record: Invalid INFO id -14336
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -13056
+Random seed for test_naive_concat: 4278025676
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out.new
+.. failed ...
+
+test_naive_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --naive /tmp/lWgqPPj34J/naive_concat.0.bcf /tmp/lWgqPPj34J/naive_concat.1.bcf /tmp/lWgqPPj34J/naive_concat.2.bcf /tmp/lWgqPPj34J/naive_concat.3.bcf /tmp/lWgqPPj34J/naive_concat.4.bcf /tmp/lWgqPPj34J/naive_concat.5.bcf /tmp/lWgqPPj34J/naive_concat.6.bcf /tmp/lWgqPPj34J/naive_concat.7.bcf /tmp/lWgqPPj34J/naive_concat.8.bcf /tmp/lWgqPPj34J/naive_concat.9.bcf | /<<PKGBUILDDIR>>/bcftools view -H
+Failed to open -: unknown file type
+
+ Non-zero status 255
+.. failed ...
+
+test_naive_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --naive /tmp/lWgqPPj34J/naive_concat.0.vcf.gz /tmp/lWgqPPj34J/naive_concat.1.vcf.gz /tmp/lWgqPPj34J/naive_concat.2.vcf.gz /tmp/lWgqPPj34J/naive_concat.3.vcf.gz /tmp/lWgqPPj34J/naive_concat.4.vcf.gz /tmp/lWgqPPj34J/naive_concat.5.vcf.gz /tmp/lWgqPPj34J/naive_concat.6.vcf.gz /tmp/lWgqPPj34J/naive_concat.7.vcf.gz /tmp/lWgqPPj34J/naive_concat.8.vcf.gz /tmp/lWgqPPj34J/naive_concat.9.vcf.gz | /<<PKGBUILDDIR>>/bcftools view -H
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.naive.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.naive.vcf.out.new
+.. failed ...
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /tmp/lWgqPPj34J/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/lWgqPPj34J/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /tmp/lWgqPPj34J/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/lWgqPPj34J/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /tmp/lWgqPPj34J/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/lWgqPPj34J/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /tmp/lWgqPPj34J/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/lWgqPPj34J/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /tmp/lWgqPPj34J/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/lWgqPPj34J/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /tmp/lWgqPPj34J/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/lWgqPPj34J/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /tmp/lWgqPPj34J/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/lWgqPPj34J/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /tmp/lWgqPPj34J/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/lWgqPPj34J/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /tmp/lWgqPPj34J/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/lWgqPPj34J/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /tmp/lWgqPPj34J/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/lWgqPPj34J/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /<<PKGBUILDDIR>>/test/empty.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/empty.vcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /tmp/lWgqPPj34J/empty.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/lWgqPPj34J/empty.bcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /tmp/lWgqPPj34J/empty.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/lWgqPPj34J/empty.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/lWgqPPj34J/rename.map -Ov /tmp/lWgqPPj34J/annotate.bcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/lWgqPPj34J/rename.map -Ob /tmp/lWgqPPj34J/annotate.bcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/lWgqPPj34J/rename.map -Ov /<<PKGBUILDDIR>>/test/annotate.vcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/lWgqPPj34J/rename.map -Ob /<<PKGBUILDDIR>>/test/annotate.vcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. /tmp/lWgqPPj34J/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- /tmp/lWgqPPj34J/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --tag PL /tmp/lWgqPPj34J/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --tag PL /tmp/lWgqPPj34J/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --vcf-ids /tmp/lWgqPPj34J/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --vcf-ids /tmp/lWgqPPj34J/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom /tmp/lWgqPPj34J/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom /tmp/lWgqPPj34J/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom --vcf-ids /tmp/lWgqPPj34J/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom --vcf-ids /tmp/lWgqPPj34J/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h -,.,. /tmp/lWgqPPj34J/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h -,.,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h .,-,. /tmp/lWgqPPj34J/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h .,-,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h .,.,- /tmp/lWgqPPj34J/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h .,.,- 2>/dev/null
+.. ok
+
+test_vcf_convert_hls2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -H /<<PKGBUILDDIR>>/test/convert.hls.gt.hap,/<<PKGBUILDDIR>>/test/convert.hls.gt.legend,/<<PKGBUILDDIR>>/test/convert.hls.gt.samples 2>/dev/null | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert_hls2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -H /<<PKGBUILDDIR>>/test/convert.hls.gt.hap,/<<PKGBUILDDIR>>/test/convert.hls.gt.legend,/<<PKGBUILDDIR>>/test/convert.hls.gt.samples -Ou 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert_hs2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample2vcf /<<PKGBUILDDIR>>/test/convert.hs.gt.hap,/<<PKGBUILDDIR>>/test/convert.hs.gt.samples 2>/dev/null | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert_hs2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample2vcf /<<PKGBUILDDIR>>/test/convert.hs.gt.hap,/<<PKGBUILDDIR>>/test/convert.hs.gt.samples -Ou 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample -,. /tmp/lWgqPPj34J/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --hapsample -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample .,- /tmp/lWgqPPj34J/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --hapsample .,- 2>/dev/null
+.. ok
+
+test_vcf_convert_gvcf:
+ /<<PKGBUILDDIR>>/bcftools convert --no-version --gvcf2vcf -f /<<PKGBUILDDIR>>/test/gvcf.fa /tmp/lWgqPPj34J/convert.gvcf.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out.new
+.. failed ...
+
+test_vcf_convert_gvcf:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/lWgqPPj34J/convert.gvcf.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --gvcf2vcf -f /<<PKGBUILDDIR>>/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out.new
+.. failed ...
+
+test_vcf_convert_tsv2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /<<PKGBUILDDIR>>/test/23andme.fa --tsv2vcf /<<PKGBUILDDIR>>/test/convert.23andme 2>/dev/null
+.. ok
+
+test_vcf_convert_tsv2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /<<PKGBUILDDIR>>/test/23andme.fa --tsv2vcf /<<PKGBUILDDIR>>/test/convert.23andme 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/lWgqPPj34J/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/lWgqPPj34J/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/lWgqPPj34J/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/lWgqPPj34J/consensus.1.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/lWgqPPj34J/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/lWgqPPj34J/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/lWgqPPj34J/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/lWgqPPj34J/consensus.2.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/lWgqPPj34J/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -I -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/lWgqPPj34J/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -I -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/lWgqPPj34J/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/lWgqPPj34J/consensus.3.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/lWgqPPj34J/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/lWgqPPj34J/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -c /tmp/lWgqPPj34J/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/lWgqPPj34J/consensus.4.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/lWgqPPj34J/consensus2.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus2.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/lWgqPPj34J/consensus2.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus2.fa -H 2 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/lWgqPPj34J/empty.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa 2>/dev/null
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -b /tmp/lWgqPPj34J/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/lWgqPPj34J/mpileup.bam.urllist 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -b /tmp/lWgqPPj34J/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/lWgqPPj34J/mpileup.cram.urllist 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_csq:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq.fa -g /<<PKGBUILDDIR>>/test/csq.gff3 /<<PKGBUILDDIR>>/test/csq.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq.gff3 ...
+Indexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq.1.out
+ /<<PKGBUILDDIR>>/test/csq.1.out.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ambiguous.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ambiguous.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ambiguous.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.gff /<<PKGBUILDDIR>>/test/csq/ENST00000593942/last-codon-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.gff ...
+Indexed 1 transcripts, 7 exons, 4 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.gff /<<PKGBUILDDIR>>/test/csq/ENST00000557788/long-overlap-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.gff /<<PKGBUILDDIR>>/test/csq/ENST00000545279/splice-region-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.gff ...
+Indexed 1 transcripts, 9 exons, 7 CDSs, 4 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff /<<PKGBUILDDIR>>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff /<<PKGBUILDDIR>>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff /<<PKGBUILDDIR>>/test/csq/ENST00000542803/splice-region.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff /<<PKGBUILDDIR>>/test/csq/ENST00000542803/splice-region.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff /<<PKGBUILDDIR>>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff /<<PKGBUILDDIR>>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.gff /<<PKGBUILDDIR>>/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.gff ...
+Indexed 1 transcripts, 7 exons, 6 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520868/long-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520795/long-inside-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520795/long-inside-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.gff /<<PKGBUILDDIR>>/test/csq/ENST00000519442/synon-splice-region-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff /<<PKGBUILDDIR>>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff /<<PKGBUILDDIR>>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.gff /<<PKGBUILDDIR>>/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.gff ...
+Indexed 1 transcripts, 26 exons, 26 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.gff /<<PKGBUILDDIR>>/test/csq/ENST00000436063/insert-before-utr.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.gff ...
+Indexed 1 transcripts, 7 exons, 7 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/snps.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/snps.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/insert3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/insert3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.gff /<<PKGBUILDDIR>>/test/csq/ENST00000420670/start-stop-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.gff ...
+Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.gff /<<PKGBUILDDIR>>/test/csq/ENST00000413103/long-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.gff ...
+Indexed 1 transcripts, 2 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.gff /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 2 UTRs
+Calling...
+[E::vcf_format] Invalid BCF, the INFO index is too large
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.gff /<<PKGBUILDDIR>>/test/csq/ENST00000409523/long-overlapping-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.gff /<<PKGBUILDDIR>>/test/csq/ENST00000390520/deletion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.gff /<<PKGBUILDDIR>>/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.gff /<<PKGBUILDDIR>>/test/csq/ENST00000381157/haploid-diploid.vcf | /<<PKGBUILDDIR>>/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 0 UTRs
+Calling...
+Warning: Skipping site with non-diploid/non-haploid genotypes at X:31180 C>T
+/bin/bash: line 1: 6982 Done /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.gff /<<PKGBUILDDIR>>/test/csq/ENST00000381157/haploid-diploid.vcf
+ 6983 Segmentation fault | /<<PKGBUILDDIR>>/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
+
+ Non-zero status 139
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff /<<PKGBUILDDIR>>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff /<<PKGBUILDDIR>>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.gff /<<PKGBUILDDIR>>/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff /<<PKGBUILDDIR>>/test/csq/ENST00000373833/boundary-insertion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff /<<PKGBUILDDIR>>/test/csq/ENST00000373833/boundary-insertion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.gff /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.gff /<<PKGBUILDDIR>>/test/csq/ENST00000357367/stop-retained.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.gff ...
+Indexed 1 transcripts, 4 exons, 3 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[E::vcf_format] Invalid BCF, the INFO index is too large
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[E::vcf_format] Invalid BCF, the INFO index is too large
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff /<<PKGBUILDDIR>>/test/csq/ENST00000329454/boundary-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff /<<PKGBUILDDIR>>/test/csq/ENST00000329454/boundary-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff /<<PKGBUILDDIR>>/test/csq/ENST00000318249/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff /<<PKGBUILDDIR>>/test/csq/ENST00000318249/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff /<<PKGBUILDDIR>>/test/csq/ENST00000303039/not-a-stop.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff /<<PKGBUILDDIR>>/test/csq/ENST00000303039/not-a-stop.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.gff /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.gff ...
+Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs
+Calling...
+[E::vcf_format] Invalid BCF, the INFO index is too large
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff /<<PKGBUILDDIR>>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff /<<PKGBUILDDIR>>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff /<<PKGBUILDDIR>>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff /<<PKGBUILDDIR>>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.gff /<<PKGBUILDDIR>>/test/csq/ENST00000256452/intron.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.gff ...
+Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.gff /<<PKGBUILDDIR>>/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff /<<PKGBUILDDIR>>/test/csq/ENST00000218032/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff /<<PKGBUILDDIR>>/test/csq/ENST00000218032/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.fa -g /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.gff /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/synon.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.gff ...
+Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs
+Calling...
+.. ok
+
+
+Number of tests:
+ total .. 728
+ passed .. 607
+ failed .. 121
+
+Makefile:246: recipe for target 'test-plugins' failed
+make[1]: *** [test-plugins] Error 1
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+dh_auto_test: make -j2 test VERBOSE=1 returned exit code 2
+debian/rules:7: recipe for target 'build-arch' failed
+make: *** [build-arch] Error 2
+dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
+--------------------------------------------------------------------------------
+Build finished at 2017-12-11T19:57:47Z
+
+Finished
+--------
+
+
++------------------------------------------------------------------------------+
+| Cleanup |
++------------------------------------------------------------------------------+
+
+Purging /<<BUILDDIR>>
+Not cleaning session: cloned chroot in use
+E: Build failure (dpkg-buildpackage died)
+
++------------------------------------------------------------------------------+
+| Summary |
++------------------------------------------------------------------------------+
+
+Build Architecture: mips
+Build Type: any
+Build-Space: 25804
+Build-Time: 10798
+Distribution: experimental
+Fail-Stage: build
+Host Architecture: mips
+Install-Time: 118
+Job: bcftools_1.6-1
+Machine Architecture: mips
+Package: bcftools
+Package-Time: 10989
+Source-Version: 1.6-1
+Space: 25804
+Status: attempted
+Version: 1.6-1
+--------------------------------------------------------------------------------
+Finished at 2017-12-11T19:57:47Z
+Build needed 03:03:09, 25804k disk space
diff --git a/bcftools_1.6-1_ppc64.log b/bcftools_1.6-1_ppc64.log
new file mode 100644
index 0000000..a5e4cb4
--- /dev/null
+++ b/bcftools_1.6-1_ppc64.log
@@ -0,0 +1,4515 @@
+
+sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ookuninushi
+
++==============================================================================+
+| bcftools 1.6-1 (ppc64) Mon, 11 Dec 2017 16:41:26 +0000 |
++==============================================================================+
+
+Package: bcftools
+Version: 1.6-1
+Source Version: 1.6-1
+Distribution: experimental
+Machine Architecture: ppc64
+Host Architecture: ppc64
+Build Architecture: ppc64
+Build Type: any
+
+I: NOTICE: Log filtering will replace 'var/run/schroot/mount/experimental-ppc64-sbuild-87648a3c-c4cc-4806-b663-70f48220f4ff' with '<<CHROOT>>'
+
++------------------------------------------------------------------------------+
+| Update chroot |
++------------------------------------------------------------------------------+
+
+Get:1 http://ftp.ports.debian.org/debian-ports unstable InRelease [37.1 kB]
+Get:2 http://ftp.debian.org/debian unstable InRelease [240 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:4 http://incoming.ports.debian.org/buildd unstable InRelease [40.0 kB]
+Get:5 http://ftp.ports.debian.org/debian-ports experimental InRelease [37.6 kB]
+Get:6 http://incoming.debian.org/debian-buildd buildd-experimental InRelease [58.9 kB]
+Get:7 http://ftp.ports.debian.org/debian-ports unreleased InRelease [40.8 kB]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [123 kB]
+Get:9 http://ftp.ports.debian.org/debian-ports unstable/main all Packages [8263 kB]
+Get:10 http://incoming.ports.debian.org/buildd experimental InRelease [40.0 kB]
+Get:11 http://ftp.debian.org/debian experimental InRelease [107 kB]
+Get:12 http://incoming.debian.org/debian-buildd buildd-experimental/main Sources [30.7 kB]
+Get:13 http://incoming.ports.debian.org/buildd unstable/main ppc64 Packages [100 kB]
+Get:14 http://ftp.debian.org/debian unstable/main Sources [7953 kB]
+Get:15 http://incoming.ports.debian.org/buildd experimental/main ppc64 Packages [24.9 kB]
+Get:16 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 Packages [20.5 MB]
+Get:17 http://ftp.debian.org/debian experimental/main Sources [262 kB]
+Get:18 http://ftp.ports.debian.org/debian-ports experimental/main ppc64 Packages [932 kB]
+Get:19 http://ftp.ports.debian.org/debian-ports experimental/main all Packages [396 kB]
+Get:20 http://ftp.ports.debian.org/debian-ports unreleased/main ppc64 Packages [1168 B]
+Fetched 39.3 MB in 9s (4306 kB/s)
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Fetch source files |
++------------------------------------------------------------------------------+
+
+
+Check APT
+---------
+
+Checking available source versions...
+
+Download source files with APT
+------------------------------
+
+Reading package lists...
+NOTICE: 'bcftools' packaging is maintained in the 'Git' version control system at:
+https://anonscm.debian.org/git/debian-med/bcftools.git
+Please use:
+git clone https://anonscm.debian.org/git/debian-med/bcftools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 2342 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (dsc) [2110 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (tar) [2333 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (diff) [6088 B]
+Fetched 2342 kB in 2s (1151 kB/s)
+Download complete and in download only mode
+I: NOTICE: Log filtering will replace 'build/bcftools-XWypqI/bcftools-1.6' with '<<PKGBUILDDIR>>'
+I: NOTICE: Log filtering will replace 'build/bcftools-XWypqI' with '<<BUILDDIR>>'
+
++------------------------------------------------------------------------------+
+| 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 '/<<BUILDDIR>>/resolver-823MIl/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:/<<BUILDDIR>>/resolver-823MIl/apt_archive ./ InRelease
+Get:2 copy:/<<BUILDDIR>>/resolver-823MIl/apt_archive ./ Release [957 B]
+Ign:3 copy:/<<BUILDDIR>>/resolver-823MIl/apt_archive ./ Release.gpg
+Get:4 copy:/<<BUILDDIR>>/resolver-823MIl/apt_archive ./ Sources [349 B]
+Get:5 copy:/<<BUILDDIR>>/resolver-823MIl/apt_archive ./ Packages [434 B]
+Fetched 1740 B in 0s (69.6 kB/s)
+Reading package lists...
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Install core build dependencies (aptitude-based resolver) |
++------------------------------------------------------------------------------+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following additional packages will be installed:
+ aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+Suggested packages:
+ aptitude-doc-en | aptitude-doc apt-xapian-index debtags tasksel
+ libcwidget-dev xapian-tools
+Recommended packages:
+ libparse-debianchangelog-perl
+The following NEW packages will be installed:
+ aptitude aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+0 upgraded, 9 newly installed, 0 to remove and 2 not upgraded.
+Need to get 5177 kB of archives.
+After this operation, 22.5 MB of additional disk space will be used.
+Get:1 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libxapian30 ppc64 1.4.5-1 [1086 kB]
+Get:2 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libsqlite3-0 ppc64 3.21.0-1 [557 kB]
+Get:3 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 aptitude-common all 0.8.10-1 [1591 kB]
+Get:4 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libboost-system1.62.0 ppc64 1.62.0+dfsg-4+b2 [33.2 kB]
+Get:5 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libboost-filesystem1.62.0 ppc64 1.62.0+dfsg-4+b2 [63.6 kB]
+Get:6 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libboost-iostreams1.62.0 ppc64 1.62.0+dfsg-4+b2 [52.3 kB]
+Get:7 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libsigc++-2.0-0v5 ppc64 2.10.0-1 [62.3 kB]
+Get:8 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libcwidget3v5 ppc64 0.5.17-6 [276 kB]
+Get:9 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 aptitude ppc64 0.8.10-1 [1456 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 5177 kB in 3s (1455 kB/s)
+Selecting previously unselected package libxapian30:ppc64.
+(Reading database ... 11584 files and directories currently installed.)
+Preparing to unpack .../0-libxapian30_1.4.5-1_ppc64.deb ...
+Unpacking libxapian30:ppc64 (1.4.5-1) ...
+Selecting previously unselected package libsqlite3-0:ppc64.
+Preparing to unpack .../1-libsqlite3-0_3.21.0-1_ppc64.deb ...
+Unpacking libsqlite3-0:ppc64 (3.21.0-1) ...
+Selecting previously unselected package aptitude-common.
+Preparing to unpack .../2-aptitude-common_0.8.10-1_all.deb ...
+Unpacking aptitude-common (0.8.10-1) ...
+Selecting previously unselected package libboost-system1.62.0:ppc64.
+Preparing to unpack .../3-libboost-system1.62.0_1.62.0+dfsg-4+b2_ppc64.deb ...
+Unpacking libboost-system1.62.0:ppc64 (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libboost-filesystem1.62.0:ppc64.
+Preparing to unpack .../4-libboost-filesystem1.62.0_1.62.0+dfsg-4+b2_ppc64.deb ...
+Unpacking libboost-filesystem1.62.0:ppc64 (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libboost-iostreams1.62.0:ppc64.
+Preparing to unpack .../5-libboost-iostreams1.62.0_1.62.0+dfsg-4+b2_ppc64.deb ...
+Unpacking libboost-iostreams1.62.0:ppc64 (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libsigc++-2.0-0v5:ppc64.
+Preparing to unpack .../6-libsigc++-2.0-0v5_2.10.0-1_ppc64.deb ...
+Unpacking libsigc++-2.0-0v5:ppc64 (2.10.0-1) ...
+Selecting previously unselected package libcwidget3v5:ppc64.
+Preparing to unpack .../7-libcwidget3v5_0.5.17-6_ppc64.deb ...
+Unpacking libcwidget3v5:ppc64 (0.5.17-6) ...
+Selecting previously unselected package aptitude.
+Preparing to unpack .../8-aptitude_0.8.10-1_ppc64.deb ...
+Unpacking aptitude (0.8.10-1) ...
+Setting up libxapian30:ppc64 (1.4.5-1) ...
+Setting up aptitude-common (0.8.10-1) ...
+Setting up libboost-iostreams1.62.0:ppc64 (1.62.0+dfsg-4+b2) ...
+Processing triggers for libc-bin (2.25-3) ...
+Setting up libsqlite3-0:ppc64 (3.21.0-1) ...
+Setting up libsigc++-2.0-0v5:ppc64 (2.10.0-1) ...
+Setting up libboost-system1.62.0:ppc64 (1.62.0+dfsg-4+b2) ...
+Setting up libboost-filesystem1.62.0:ppc64 (1.62.0+dfsg-4+b2) ...
+Setting up libcwidget3v5:ppc64 (0.5.17-6) ...
+Setting up aptitude (0.8.10-1) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode
+Processing triggers for libc-bin (2.25-3) ...
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-core-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-core-dummy:ppc64
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+0 packages upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
+Need to get 848 B of archives. After unpacking 0 B will be used.
+Writing extended state information...
+Get: 1 copy:/<<BUILDDIR>>/resolver-823MIl/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
+Fetched 848 B in 0s (0 B/s)
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11838 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+
++------------------------------------------------------------------------------+
+| Check architectures |
++------------------------------------------------------------------------------+
+
+Arch check ok (ppc64 included in any)
+
++------------------------------------------------------------------------------+
+| Install package build dependencies |
++------------------------------------------------------------------------------+
+
+
+Setup apt archive
+-----------------
+
+Merged Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+Filtered Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<<BUILDDIR>>/resolver-823MIl/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:/<<BUILDDIR>>/resolver-823MIl/apt_archive ./ InRelease
+Get:2 copy:/<<BUILDDIR>>/resolver-823MIl/apt_archive ./ Release [963 B]
+Ign:3 copy:/<<BUILDDIR>>/resolver-823MIl/apt_archive ./ Release.gpg
+Get:4 copy:/<<BUILDDIR>>/resolver-823MIl/apt_archive ./ Sources [546 B]
+Get:5 copy:/<<BUILDDIR>>/resolver-823MIl/apt_archive ./ Packages [616 B]
+Fetched 2125 B in 0s (74.5 kB/s)
+Reading package lists...
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Install bcftools build dependencies (aptitude-based resolver) |
++------------------------------------------------------------------------------+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+aptitude is already the newest version (0.8.10-1).
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-bcftools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-bcftool [...]
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libbz2-dev{a} libcroco3{a} libcurl3-gnutls{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu57{a} libio-pty-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} l [...]
+The following packages are RECOMMENDED but will NOT be installed:
+ bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx-cur publicsuffix shared-mime-info wget xdg-user-dirs
+0 packages upgraded, 56 newly installed, 0 to remove and 2 not upgraded.
+Need to get 25.8 MB of archives. After unpacking 102 MB will be used.
+Writing extended state information...
+Get: 1 copy:/<<BUILDDIR>>/resolver-823MIl/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [904 B]
+Get: 2 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 groff-base ppc64 1.22.3-9 [1283 kB]
+Get: 3 http://incoming.ports.debian.org/buildd unstable/main ppc64 libhts2 ppc64 1.5-6 [289 kB]
+Get: 4 http://incoming.ports.debian.org/buildd unstable/main ppc64 tabix ppc64 1.5-6 [299 kB]
+Get: 5 http://incoming.ports.debian.org/buildd unstable/main ppc64 libhts-dev ppc64 1.5-6 [367 kB]
+Get: 6 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libbsd0 ppc64 0.8.6-3 [92.0 kB]
+Get: 7 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libncurses5 ppc64 6.0+20171125-1 [92.3 kB]
+Get: 8 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 bsdmainutils ppc64 9.0.14 [187 kB]
+Get: 9 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libpipeline1 ppc64 1.5.0-1 [28.2 kB]
+Get: 10 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 man-db ppc64 2.7.6.1-4 [1035 kB]
+Get: 11 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libssl1.1 ppc64 1.1.0g-2 [1054 kB]
+Get: 12 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libmagic-mgc ppc64 1:5.32-1 [226 kB]
+Get: 13 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libmagic1 ppc64 1:5.32-1 [111 kB]
+Get: 14 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 file ppc64 1:5.32-1 [64.7 kB]
+Get: 15 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 gettext-base ppc64 0.19.8.1-4 [121 kB]
+Get: 16 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libkeyutils1 ppc64 1.5.9-9.2 [13.1 kB]
+Get: 17 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libkrb5support0 ppc64 1.15.2-2 [62.6 kB]
+Get: 18 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libk5crypto3 ppc64 1.15.2-2 [125 kB]
+Get: 19 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libkrb5-3 ppc64 1.15.2-2 [304 kB]
+Get: 20 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libgssapi-krb5-2 ppc64 1.15.2-2 [151 kB]
+Get: 21 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libsasl2-modules-db ppc64 2.1.27~101-g0780600+dfsg-3 [68.1 kB]
+Get: 22 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libsasl2-2 ppc64 2.1.27~101-g0780600+dfsg-3 [102 kB]
+Get: 23 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libldap-common all 2.4.45+dfsg-1 [87.0 kB]
+Get: 24 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libldap-2.4-2 ppc64 2.4.45+dfsg-1 [208 kB]
+Get: 25 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libicu57 ppc64 57.1-8 [7670 kB]
+Get: 26 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libxml2 ppc64 2.9.4+dfsg1-5.1 [669 kB]
+Get: 27 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libsigsegv2 ppc64 2.11-1 [29.9 kB]
+Get: 28 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 m4 ppc64 1.4.18-1 [194 kB]
+Get: 29 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 autoconf all 2.69-11 [341 kB]
+Get: 30 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 autotools-dev all 20161112.1+nmu1 [74.2 kB]
+Get: 31 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 automake all 1:1.15.1-3 [736 kB]
+Get: 32 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 autopoint all 0.19.8.1-4 [434 kB]
+Get: 33 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libtool all 2.4.6-2 [545 kB]
+Get: 34 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 dh-autoreconf all 15 [16.2 kB]
+Get: 35 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libarchive-zip-perl all 1.59-1 [95.5 kB]
+Get: 36 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
+Get: 37 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get: 38 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 dh-strip-nondeterminism all 0.040-1 [11.8 kB]
+Get: 39 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libglib2.0-0 ppc64 2.54.2-1 [2708 kB]
+Get: 40 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libcroco3 ppc64 0.6.12-1 [134 kB]
+Get: 41 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 gettext ppc64 0.19.8.1-4 [1265 kB]
+Get: 42 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get: 43 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 po-debconf all 1.0.20 [247 kB]
+Get: 44 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 debhelper all 10.10.9 [975 kB]
+Get: 45 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libbz2-dev ppc64 1.0.6-8.1 [32.6 kB]
+Get: 46 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libnghttp2-14 ppc64 1.28.0-1 [81.9 kB]
+Get: 47 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libpsl5 ppc64 0.19.1-4 [44.8 kB]
+Get: 48 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 librtmp1 ppc64 2.4+20151223.gitfa8646d.1-1 [57.6 kB]
+Get: 49 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libssh2-1 ppc64 1.8.0-1 [133 kB]
+Get: 50 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libcurl3-gnutls ppc64 7.57.0-1 [295 kB]
+Get: 51 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libgslcblas0 ppc64 2.4+dfsg-6 [94.3 kB]
+Get: 52 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libgsl23 ppc64 2.4+dfsg-6 [845 kB]
+Get: 53 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libgsl-dev ppc64 2.4+dfsg-6 [1077 kB]
+Get: 54 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 liblzma-dev ppc64 5.2.2-1.3 [291 kB]
+Get: 55 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 libio-pty-perl ppc64 1:1.08-1.1+b5 [33.2 kB]
+Get: 56 http://ftp.ports.debian.org/debian-ports unstable/main ppc64 zlib1g-dev ppc64 1:1.2.8.dfsg-5 [202 kB]
+Fetched 25.8 MB in 5s (4627 kB/s)
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package groff-base.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11838 files and directories currently installed.)
+Preparing to unpack .../00-groff-base_1.22.3-9_ppc64.deb ...
+Unpacking groff-base (1.22.3-9) ...
+Selecting previously unselected package libbsd0:ppc64.
+Preparing to unpack .../01-libbsd0_0.8.6-3_ppc64.deb ...
+Unpacking libbsd0:ppc64 (0.8.6-3) ...
+Selecting previously unselected package libncurses5:ppc64.
+Preparing to unpack .../02-libncurses5_6.0+20171125-1_ppc64.deb ...
+Unpacking libncurses5:ppc64 (6.0+20171125-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../03-bsdmainutils_9.0.14_ppc64.deb ...
+Unpacking bsdmainutils (9.0.14) ...
+Selecting previously unselected package libpipeline1:ppc64.
+Preparing to unpack .../04-libpipeline1_1.5.0-1_ppc64.deb ...
+Unpacking libpipeline1:ppc64 (1.5.0-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../05-man-db_2.7.6.1-4_ppc64.deb ...
+Unpacking man-db (2.7.6.1-4) ...
+Selecting previously unselected package libssl1.1:ppc64.
+Preparing to unpack .../06-libssl1.1_1.1.0g-2_ppc64.deb ...
+Unpacking libssl1.1:ppc64 (1.1.0g-2) ...
+Selecting previously unselected package libmagic-mgc.
+Preparing to unpack .../07-libmagic-mgc_1%3a5.32-1_ppc64.deb ...
+Unpacking libmagic-mgc (1:5.32-1) ...
+Selecting previously unselected package libmagic1:ppc64.
+Preparing to unpack .../08-libmagic1_1%3a5.32-1_ppc64.deb ...
+Unpacking libmagic1:ppc64 (1:5.32-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../09-file_1%3a5.32-1_ppc64.deb ...
+Unpacking file (1:5.32-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../10-gettext-base_0.19.8.1-4_ppc64.deb ...
+Unpacking gettext-base (0.19.8.1-4) ...
+Selecting previously unselected package libkeyutils1:ppc64.
+Preparing to unpack .../11-libkeyutils1_1.5.9-9.2_ppc64.deb ...
+Unpacking libkeyutils1:ppc64 (1.5.9-9.2) ...
+Selecting previously unselected package libkrb5support0:ppc64.
+Preparing to unpack .../12-libkrb5support0_1.15.2-2_ppc64.deb ...
+Unpacking libkrb5support0:ppc64 (1.15.2-2) ...
+Selecting previously unselected package libk5crypto3:ppc64.
+Preparing to unpack .../13-libk5crypto3_1.15.2-2_ppc64.deb ...
+Unpacking libk5crypto3:ppc64 (1.15.2-2) ...
+Selecting previously unselected package libkrb5-3:ppc64.
+Preparing to unpack .../14-libkrb5-3_1.15.2-2_ppc64.deb ...
+Unpacking libkrb5-3:ppc64 (1.15.2-2) ...
+Selecting previously unselected package libgssapi-krb5-2:ppc64.
+Preparing to unpack .../15-libgssapi-krb5-2_1.15.2-2_ppc64.deb ...
+Unpacking libgssapi-krb5-2:ppc64 (1.15.2-2) ...
+Selecting previously unselected package libsasl2-modules-db:ppc64.
+Preparing to unpack .../16-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3_ppc64.deb ...
+Unpacking libsasl2-modules-db:ppc64 (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libsasl2-2:ppc64.
+Preparing to unpack .../17-libsasl2-2_2.1.27~101-g0780600+dfsg-3_ppc64.deb ...
+Unpacking libsasl2-2:ppc64 (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libldap-common.
+Preparing to unpack .../18-libldap-common_2.4.45+dfsg-1_all.deb ...
+Unpacking libldap-common (2.4.45+dfsg-1) ...
+Selecting previously unselected package libldap-2.4-2:ppc64.
+Preparing to unpack .../19-libldap-2.4-2_2.4.45+dfsg-1_ppc64.deb ...
+Unpacking libldap-2.4-2:ppc64 (2.4.45+dfsg-1) ...
+Selecting previously unselected package libicu57:ppc64.
+Preparing to unpack .../20-libicu57_57.1-8_ppc64.deb ...
+Unpacking libicu57:ppc64 (57.1-8) ...
+Selecting previously unselected package libxml2:ppc64.
+Preparing to unpack .../21-libxml2_2.9.4+dfsg1-5.1_ppc64.deb ...
+Unpacking libxml2:ppc64 (2.9.4+dfsg1-5.1) ...
+Selecting previously unselected package libsigsegv2:ppc64.
+Preparing to unpack .../22-libsigsegv2_2.11-1_ppc64.deb ...
+Unpacking libsigsegv2:ppc64 (2.11-1) ...
+Selecting previously unselected package m4.
+Preparing to unpack .../23-m4_1.4.18-1_ppc64.deb ...
+Unpacking m4 (1.4.18-1) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../24-autoconf_2.69-11_all.deb ...
+Unpacking autoconf (2.69-11) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../25-autotools-dev_20161112.1+nmu1_all.deb ...
+Unpacking autotools-dev (20161112.1+nmu1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../26-automake_1%3a1.15.1-3_all.deb ...
+Unpacking automake (1:1.15.1-3) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../27-autopoint_0.19.8.1-4_all.deb ...
+Unpacking autopoint (0.19.8.1-4) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../28-libtool_2.4.6-2_all.deb ...
+Unpacking libtool (2.4.6-2) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../29-dh-autoreconf_15_all.deb ...
+Unpacking dh-autoreconf (15) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../30-libarchive-zip-perl_1.59-1_all.deb ...
+Unpacking libarchive-zip-perl (1.59-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../31-libfile-stripnondeterminism-perl_0.040-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.040-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../32-libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../33-dh-strip-nondeterminism_0.040-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.040-1) ...
+Selecting previously unselected package libglib2.0-0:ppc64.
+Preparing to unpack .../34-libglib2.0-0_2.54.2-1_ppc64.deb ...
+Unpacking libglib2.0-0:ppc64 (2.54.2-1) ...
+Selecting previously unselected package libcroco3:ppc64.
+Preparing to unpack .../35-libcroco3_0.6.12-1_ppc64.deb ...
+Unpacking libcroco3:ppc64 (0.6.12-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../36-gettext_0.19.8.1-4_ppc64.deb ...
+Unpacking gettext (0.19.8.1-4) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../37-intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../38-po-debconf_1.0.20_all.deb ...
+Unpacking po-debconf (1.0.20) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../39-debhelper_10.10.9_all.deb ...
+Unpacking debhelper (10.10.9) ...
+Selecting previously unselected package libbz2-dev:ppc64.
+Preparing to unpack .../40-libbz2-dev_1.0.6-8.1_ppc64.deb ...
+Unpacking libbz2-dev:ppc64 (1.0.6-8.1) ...
+Selecting previously unselected package libnghttp2-14:ppc64.
+Preparing to unpack .../41-libnghttp2-14_1.28.0-1_ppc64.deb ...
+Unpacking libnghttp2-14:ppc64 (1.28.0-1) ...
+Selecting previously unselected package libpsl5:ppc64.
+Preparing to unpack .../42-libpsl5_0.19.1-4_ppc64.deb ...
+Unpacking libpsl5:ppc64 (0.19.1-4) ...
+Selecting previously unselected package librtmp1:ppc64.
+Preparing to unpack .../43-librtmp1_2.4+20151223.gitfa8646d.1-1_ppc64.deb ...
+Unpacking librtmp1:ppc64 (2.4+20151223.gitfa8646d.1-1) ...
+Selecting previously unselected package libssh2-1:ppc64.
+Preparing to unpack .../44-libssh2-1_1.8.0-1_ppc64.deb ...
+Unpacking libssh2-1:ppc64 (1.8.0-1) ...
+Selecting previously unselected package libcurl3-gnutls:ppc64.
+Preparing to unpack .../45-libcurl3-gnutls_7.57.0-1_ppc64.deb ...
+Unpacking libcurl3-gnutls:ppc64 (7.57.0-1) ...
+Selecting previously unselected package libgslcblas0:ppc64.
+Preparing to unpack .../46-libgslcblas0_2.4+dfsg-6_ppc64.deb ...
+Unpacking libgslcblas0:ppc64 (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl23:ppc64.
+Preparing to unpack .../47-libgsl23_2.4+dfsg-6_ppc64.deb ...
+Unpacking libgsl23:ppc64 (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl-dev.
+Preparing to unpack .../48-libgsl-dev_2.4+dfsg-6_ppc64.deb ...
+Unpacking libgsl-dev (2.4+dfsg-6) ...
+Selecting previously unselected package libhts2:ppc64.
+Preparing to unpack .../49-libhts2_1.5-6_ppc64.deb ...
+Unpacking libhts2:ppc64 (1.5-6) ...
+Selecting previously unselected package liblzma-dev:ppc64.
+Preparing to unpack .../50-liblzma-dev_5.2.2-1.3_ppc64.deb ...
+Unpacking liblzma-dev:ppc64 (5.2.2-1.3) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../51-tabix_1.5-6_ppc64.deb ...
+Unpacking tabix (1.5-6) ...
+Selecting previously unselected package libhts-dev:ppc64.
+Preparing to unpack .../52-libhts-dev_1.5-6_ppc64.deb ...
+Unpacking libhts-dev:ppc64 (1.5-6) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../53-libio-pty-perl_1%3a1.08-1.1+b5_ppc64.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b5) ...
+Selecting previously unselected package zlib1g-dev:ppc64.
+Preparing to unpack .../54-zlib1g-dev_1%3a1.2.8.dfsg-5_ppc64.deb ...
+Unpacking zlib1g-dev:ppc64 (1:1.2.8.dfsg-5) ...
+Selecting previously unselected package sbuild-build-depends-bcftools-dummy.
+Preparing to unpack .../55-sbuild-build-depends-bcftools-dummy_0.invalid.0_ppc64.deb ...
+Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Setting up libncurses5:ppc64 (6.0+20171125-1) ...
+Setting up libbz2-dev:ppc64 (1.0.6-8.1) ...
+Setting up libarchive-zip-perl (1.59-1) ...
+Setting up libnghttp2-14:ppc64 (1.28.0-1) ...
+Setting up libio-pty-perl (1:1.08-1.1+b5) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libsigsegv2:ppc64 (2.11-1) ...
+Setting up libldap-common (2.4.45+dfsg-1) ...
+Setting up libpsl5:ppc64 (0.19.1-4) ...
+Setting up groff-base (1.22.3-9) ...
+Setting up libglib2.0-0:ppc64 (2.54.2-1) ...
+No schema files found: doing nothing.
+Setting up libsasl2-modules-db:ppc64 (2.1.27~101-g0780600+dfsg-3) ...
+Setting up libsasl2-2:ppc64 (2.1.27~101-g0780600+dfsg-3) ...
+Setting up gettext-base (0.19.8.1-4) ...
+Setting up libpipeline1:ppc64 (1.5.0-1) ...
+Setting up librtmp1:ppc64 (2.4+20151223.gitfa8646d.1-1) ...
+Setting up m4 (1.4.18-1) ...
+Setting up libicu57:ppc64 (57.1-8) ...
+Setting up libbsd0:ppc64 (0.8.6-3) ...
+Setting up libxml2:ppc64 (2.9.4+dfsg1-5.1) ...
+Setting up libmagic-mgc (1:5.32-1) ...
+Setting up libmagic1:ppc64 (1:5.32-1) ...
+Setting up libcroco3:ppc64 (0.6.12-1) ...
+Setting up libssh2-1:ppc64 (1.8.0-1) ...
+Processing triggers for libc-bin (2.25-3) ...
+Setting up autotools-dev (20161112.1+nmu1) ...
+Setting up libldap-2.4-2:ppc64 (2.4.45+dfsg-1) ...
+Setting up libssl1.1:ppc64 (1.1.0g-2) ...
+Setting up liblzma-dev:ppc64 (5.2.2-1.3) ...
+Setting up libkeyutils1:ppc64 (1.5.9-9.2) ...
+Setting up bsdmainutils (9.0.14) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libgslcblas0:ppc64 (2.4+dfsg-6) ...
+Setting up autopoint (0.19.8.1-4) ...
+Setting up zlib1g-dev:ppc64 (1:1.2.8.dfsg-5) ...
+Setting up libfile-stripnondeterminism-perl (0.040-1) ...
+Setting up libgsl23:ppc64 (2.4+dfsg-6) ...
+Setting up gettext (0.19.8.1-4) ...
+Setting up libgsl-dev (2.4+dfsg-6) ...
+Setting up autoconf (2.69-11) ...
+Setting up file (1:5.32-1) ...
+Setting up libkrb5support0:ppc64 (1.15.2-2) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up automake (1:1.15.1-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
+Setting up man-db (2.7.6.1-4) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libtool (2.4.6-2) ...
+Setting up libk5crypto3:ppc64 (1.15.2-2) ...
+Setting up po-debconf (1.0.20) ...
+Setting up libkrb5-3:ppc64 (1.15.2-2) ...
+Setting up libgssapi-krb5-2:ppc64 (1.15.2-2) ...
+Setting up libcurl3-gnutls:ppc64 (7.57.0-1) ...
+Setting up tabix (1.5-6) ...
+Setting up libhts2:ppc64 (1.5-6) ...
+Setting up libhts-dev:ppc64 (1.5-6) ...
+Setting up dh-autoreconf (15) ...
+Setting up dh-strip-nondeterminism (0.040-1) ...
+Setting up debhelper (10.10.9) ...
+Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.25-3) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+
++------------------------------------------------------------------------------+
+| Build environment |
++------------------------------------------------------------------------------+
+
+Kernel: Linux 4.13.0-1-powerpc64 ppc64 (ppc64)
+Toolchain package versions: binutils_2.29.1-11 dpkg-dev_1.19.0.4 g++-7_7.2.0-17 gcc-7_7.2.0-17 libc6-dev_2.25-3 libstdc++-7-dev_7.2.0-17 libstdc++6_7.2.0-17 linux-libc-dev_4.14.2-1
+Package versions: adduser_3.116 apt_1.6~alpha5 aptitude_0.8.10-1 aptitude-common_0.8.10-1 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-11 binutils-common_2.29.1-11 binutils-powerpc64-linux-gnu_2.29.1-11 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 coreutils_8.28-1 cpp_4:7.2.0-1d1 cpp-7_7.2.0-17 dash_0.5.8-2.5 debconf_1.5.65 debhelper_10.10.9 debian-arch [...]
+
++------------------------------------------------------------------------------+
+| Build |
++------------------------------------------------------------------------------+
+
+
+Unpack source
+-------------
+
+gpgv: unknown type of key resource 'trustedkeys.kbx'
+gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
+gpgv: Signature made Mon Dec 11 14:53:09 2017 UTC
+gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
+gpgv: issuer "tillea at rki.de"
+gpgv: Can't check signature: No public key
+dpkg-source: warning: failed to verify signature on ./bcftools_1.6-1.dsc
+dpkg-source: info: extracting bcftools in /<<PKGBUILDDIR>>
+dpkg-source: info: unpacking bcftools_1.6.orig.tar.gz
+dpkg-source: info: unpacking bcftools_1.6-1.debian.tar.xz
+dpkg-source: info: applying tests-pluginpath.patch
+dpkg-source: info: applying test-regidx-unsigned-char.patch
+dpkg-source: info: applying fix-test_vcf_query.patch
+
+Check disk space
+----------------
+
+Sufficient free space for build
+
+User Environment
+----------------
+
+APT_CONFIG=/var/lib/sbuild/apt.conf
+DEB_BUILD_OPTIONS=parallel=16
+HOME=/sbuild-nonexistent
+LC_ALL=POSIX
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=experimental-ppc64-sbuild
+SCHROOT_CHROOT_NAME=experimental-ppc64-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=113
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=experimental-ppc64-sbuild-87648a3c-c4cc-4806-b663-70f48220f4ff
+SCHROOT_UID=109
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
+
+dpkg-buildpackage
+-----------------
+
+dpkg-buildpackage: info: source package bcftools
+dpkg-buildpackage: info: source version 1.6-1
+dpkg-buildpackage: info: source distribution experimental
+ dpkg-source --before-build bcftools-1.6
+dpkg-buildpackage: info: host architecture ppc64
+ fakeroot debian/rules clean
+rm -f config.mk && touch config.mk
+dh clean --parallel
+ dh_auto_clean
+ make -j16 distclean
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+rm -f test/*.o test/*~
+rm -f plugins/*.so plugins/*.P
+rm -rf plugins/*.dSYM
+rm -f gmon.out *.o *~ version.h plugins/*.so plugins/*.P
+rm -rf *.dSYM plugins/*.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 '/<<PKGBUILDDIR>>'
+ dh_clean
+ debian/rules build-arch
+dh build-arch --parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_autoreconf
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+rm -f config.mk && touch config.mk
+export MAKEFLAGS="-s"; dh_autoreconf
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+dh_auto_configure -- \
+--with-htslib=system \
+--enable-gsl \
+--with-cblas=gslcblas \
+--with-bcf-plugin-dir=/usr/lib/powerpc64-linux-gnu/bcftools
+ ./configure --build=powerpc64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/powerpc64-linux-gnu --libexecdir=\${prefix}/lib/powerpc64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/powerpc64-linux-gnu/bcftools
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... no
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking shared library type... plain .so
+checking for library containing dlopen... -ldl
+checking if the compiler accepts -rdynamic... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ dh_auto_build -a -O--parallel
+ make -j16
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+echo '#define BCFTOOLS_VERSION "1.6"' > version.h
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/powerpc64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c
+gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl
+gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -ldl -ldl
+gcc -rdynamic -pthread -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 vcfplugin.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 ccall.o em.o prob1.o kmin.o -l [...]
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ dh_auto_test -a -O--parallel
+ make -j16 test VERBOSE=1
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+./test/test-rbuf
+Inserted 1-9 starting at offset 5:
+ 5 6 7 8 9 0 1 2 3
+ 1 2 3 4 5 6 7 8 9
+4th is 4
+Deleting 1-2:
+ 7 8 9 0 1 2 3
+ 3 4 5 6 7 8 9
+Prepending 0-8:
+ 8 9 0 1 2 3 4 5 6 7
+ 8 7 6 5 4 3 2 1 0 3
+Expanding:
+ 8 9 10 11 12 13 14 15 16 17
+ 8 7 6 5 4 3 2 1 0 3
+./test/test-regidx
+REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix=
+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/kNTRd7dAzQ/merge.a.vcf.gz 2:3199812-3199812
+.. ok
+
+test_tabix:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/kNTRd7dAzQ/merge.a.bcf 2:3199812-3199812
+.. ok
+
+test_tabix:
+ tabix /tmp/kNTRd7dAzQ/merge.a.vcf.gz 1:3000151-3000151
+.. ok
+
+test_tabix:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/kNTRd7dAzQ/merge.a.bcf 1:3000151-3000151
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/kNTRd7dAzQ/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/kNTRd7dAzQ/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/kNTRd7dAzQ/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/kNTRd7dAzQ/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/kNTRd7dAzQ/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/kNTRd7dAzQ/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/kNTRd7dAzQ/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/kNTRd7dAzQ/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/kNTRd7dAzQ/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/kNTRd7dAzQ/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/kNTRd7dAzQ/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/kNTRd7dAzQ/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/kNTRd7dAzQ/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/kNTRd7dAzQ/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/kNTRd7dAzQ/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/kNTRd7dAzQ/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/kNTRd7dAzQ/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/kNTRd7dAzQ/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/kNTRd7dAzQ/empty.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/kNTRd7dAzQ/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/kNTRd7dAzQ/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/kNTRd7dAzQ/empty.bcf
+.. ok
+
+test_vcf_check:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/kNTRd7dAzQ/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check_merge:
+ /<<PKGBUILDDIR>>/misc/plot-vcfstats -m /tmp/kNTRd7dAzQ/check.1.chk /tmp/kNTRd7dAzQ/check.2.chk /tmp/kNTRd7dAzQ/check.3.chk /tmp/kNTRd7dAzQ/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/kNTRd7dAzQ/stats.a.vcf.gz /tmp/kNTRd7dAzQ/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s B /tmp/kNTRd7dAzQ/stats.a.vcf.gz /tmp/kNTRd7dAzQ/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/kNTRd7dAzQ/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 /tmp/kNTRd7dAzQ/isec.a.vcf.gz /tmp/kNTRd7dAzQ/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 /tmp/kNTRd7dAzQ/isec.a.vcf.gz /tmp/kNTRd7dAzQ/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/kNTRd7dAzQ/isec.a.vcf.gz /tmp/kNTRd7dAzQ/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/kNTRd7dAzQ/isec.a.vcf.gz /tmp/kNTRd7dAzQ/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -c both /tmp/kNTRd7dAzQ/isec.a.vcf.gz /tmp/kNTRd7dAzQ/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -c both /tmp/kNTRd7dAzQ/isec.a.vcf.gz /tmp/kNTRd7dAzQ/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -c any /tmp/kNTRd7dAzQ/isec.a.vcf.gz /tmp/kNTRd7dAzQ/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -c any /tmp/kNTRd7dAzQ/isec.a.vcf.gz /tmp/kNTRd7dAzQ/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -C -c any /tmp/kNTRd7dAzQ/isec.a.vcf.gz /tmp/kNTRd7dAzQ/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -C -c any /tmp/kNTRd7dAzQ/isec.a.vcf.gz /tmp/kNTRd7dAzQ/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec2:
+ /<<PKGBUILDDIR>>/bcftools isec --no-version -T /tmp/kNTRd7dAzQ/isec.tab.gz /tmp/kNTRd7dAzQ/isec.a.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/isec.tab.out
+ /<<PKGBUILDDIR>>/test/isec.tab.out.new
+.. failed ...
+
+test_vcf_isec2:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -T /tmp/kNTRd7dAzQ/isec.tab.gz /tmp/kNTRd7dAzQ/isec.a.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/isec.tab.out
+ /<<PKGBUILDDIR>>/test/isec.tab.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples /tmp/kNTRd7dAzQ/merge.a.vcf.gz /tmp/kNTRd7dAzQ/merge.b.vcf.gz /tmp/kNTRd7dAzQ/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.out
+ /<<PKGBUILDDIR>>/test/merge.abc.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples /tmp/kNTRd7dAzQ/merge.a.vcf.gz /tmp/kNTRd7dAzQ/merge.b.vcf.gz /tmp/kNTRd7dAzQ/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.out
+ /<<PKGBUILDDIR>>/test/merge.abc.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -Fx /tmp/kNTRd7dAzQ/merge.a.vcf.gz /tmp/kNTRd7dAzQ/merge.b.vcf.gz /tmp/kNTRd7dAzQ/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -Fx /tmp/kNTRd7dAzQ/merge.a.vcf.gz /tmp/kNTRd7dAzQ/merge.b.vcf.gz /tmp/kNTRd7dAzQ/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -0 /tmp/kNTRd7dAzQ/merge.a.vcf.gz /tmp/kNTRd7dAzQ/merge.b.vcf.gz /tmp/kNTRd7dAzQ/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -0 /tmp/kNTRd7dAzQ/merge.a.vcf.gz /tmp/kNTRd7dAzQ/merge.b.vcf.gz /tmp/kNTRd7dAzQ/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m none /tmp/kNTRd7dAzQ/merge.2.a.vcf.gz /tmp/kNTRd7dAzQ/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.none.out
+ /<<PKGBUILDDIR>>/test/merge.2.none.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m none /tmp/kNTRd7dAzQ/merge.2.a.vcf.gz /tmp/kNTRd7dAzQ/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.none.out
+ /<<PKGBUILDDIR>>/test/merge.2.none.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m both /tmp/kNTRd7dAzQ/merge.2.a.vcf.gz /tmp/kNTRd7dAzQ/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.both.out
+ /<<PKGBUILDDIR>>/test/merge.2.both.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m both /tmp/kNTRd7dAzQ/merge.2.a.vcf.gz /tmp/kNTRd7dAzQ/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.both.out
+ /<<PKGBUILDDIR>>/test/merge.2.both.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m all /tmp/kNTRd7dAzQ/merge.2.a.vcf.gz /tmp/kNTRd7dAzQ/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.all.out
+ /<<PKGBUILDDIR>>/test/merge.2.all.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m all /tmp/kNTRd7dAzQ/merge.2.a.vcf.gz /tmp/kNTRd7dAzQ/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.all.out
+ /<<PKGBUILDDIR>>/test/merge.2.all.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/kNTRd7dAzQ/merge.3.a.vcf.gz /tmp/kNTRd7dAzQ/merge.3.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.3.out
+ /<<PKGBUILDDIR>>/test/merge.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/kNTRd7dAzQ/merge.3.a.vcf.gz /tmp/kNTRd7dAzQ/merge.3.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.3.out
+ /<<PKGBUILDDIR>>/test/merge.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m id /tmp/kNTRd7dAzQ/merge.4.a.vcf.gz /tmp/kNTRd7dAzQ/merge.4.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.4.out
+ /<<PKGBUILDDIR>>/test/merge.4.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m id /tmp/kNTRd7dAzQ/merge.4.a.vcf.gz /tmp/kNTRd7dAzQ/merge.4.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.4.out
+ /<<PKGBUILDDIR>>/test/merge.4.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - /tmp/kNTRd7dAzQ/gvcf.merge.1.vcf.gz /tmp/kNTRd7dAzQ/gvcf.merge.2.vcf.gz /tmp/kNTRd7dAzQ/gvcf.merge.3.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - /tmp/kNTRd7dAzQ/gvcf.merge.1.vcf.gz /tmp/kNTRd7dAzQ/gvcf.merge.2.vcf.gz /tmp/kNTRd7dAzQ/gvcf.merge.3.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - /tmp/kNTRd7dAzQ/merge.gvcf.2.a.vcf.gz /tmp/kNTRd7dAzQ/merge.gvcf.2.b.vcf.gz /tmp/kNTRd7dAzQ/merge.gvcf.2.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - /tmp/kNTRd7dAzQ/merge.gvcf.2.a.vcf.gz /tmp/kNTRd7dAzQ/merge.gvcf.2.b.vcf.gz /tmp/kNTRd7dAzQ/merge.gvcf.2.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - -i SRC:join /tmp/kNTRd7dAzQ/merge.gvcf.3.a.vcf.gz /tmp/kNTRd7dAzQ/merge.gvcf.3.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/kNTRd7dAzQ/merge.gvcf.3.a.vcf.gz /tmp/kNTRd7dAzQ/merge.gvcf.3.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version /tmp/kNTRd7dAzQ/merge.5.a.vcf.gz /tmp/kNTRd7dAzQ/merge.5.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob /tmp/kNTRd7dAzQ/merge.5.a.vcf.gz /tmp/kNTRd7dAzQ/merge.5.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/kNTRd7dAzQ/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XRI\n' -i'XRI[*]>1111'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' /tmp/kNTRd7dAzQ/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/kNTRd7dAzQ/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/kNTRd7dAzQ/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10' /tmp/kNTRd7dAzQ/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/kNTRd7dAzQ/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/kNTRd7dAzQ/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/kNTRd7dAzQ/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/kNTRd7dAzQ/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/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/kNTRd7dAzQ/view.vectors.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/query.12.out
+ /<<PKGBUILDDIR>>/test/query.12.out.new
+.. failed ...
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/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'
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/query.12.out
+ /<<PKGBUILDDIR>>/test/query.12.out.new
+.. failed ...
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' /tmp/kNTRd7dAzQ/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' /tmp/kNTRd7dAzQ/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' /tmp/kNTRd7dAzQ/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' /tmp/kNTRd7dAzQ/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/kNTRd7dAzQ/query.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%LINE' /tmp/kNTRd7dAzQ/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%LINE'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/kNTRd7dAzQ/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/kNTRd7dAzQ/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/kNTRd7dAzQ/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/kNTRd7dAzQ/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/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/kNTRd7dAzQ/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/filter-missing-floats.vcf.gz | /<<PKGBUILDDIR>>/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:
+ /<<PKGBUILDDIR>>/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/kNTRd7dAzQ/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/filter-missing-floats.vcf.gz | /<<PKGBUILDDIR>>/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:
+ /<<PKGBUILDDIR>>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/kNTRd7dAzQ/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/kNTRd7dAzQ/query.filter.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/query.filter.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5'
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -cx -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/kNTRd7dAzQ/norm.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.out
+ /<<PKGBUILDDIR>>/test/norm.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -cx -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/kNTRd7dAzQ/norm.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.out
+ /<<PKGBUILDDIR>>/test/norm.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- /tmp/kNTRd7dAzQ/norm.split.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.split.out
+ /<<PKGBUILDDIR>>/test/norm.split.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- /tmp/kNTRd7dAzQ/norm.split.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.split.out
+ /<<PKGBUILDDIR>>/test/norm.split.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- /tmp/kNTRd7dAzQ/norm.split.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- /tmp/kNTRd7dAzQ/norm.split.2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/kNTRd7dAzQ/norm.split.vcf.gz 2>/dev/null
+
+ Non-zero status 255
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/kNTRd7dAzQ/norm.split.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/kNTRd7dAzQ/norm.merge.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.out
+ /<<PKGBUILDDIR>>/test/norm.merge.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/kNTRd7dAzQ/norm.merge.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.out
+ /<<PKGBUILDDIR>>/test/norm.merge.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/kNTRd7dAzQ/norm.merge.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/kNTRd7dAzQ/norm.merge.2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/kNTRd7dAzQ/norm.merge.3.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/kNTRd7dAzQ/norm.merge.3.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.'
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ -s /tmp/kNTRd7dAzQ/norm.merge.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ -s /tmp/kNTRd7dAzQ/norm.merge.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -Nc s -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/kNTRd7dAzQ/norm.setref.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -Nc s -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/kNTRd7dAzQ/norm.setref.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/kNTRd7dAzQ/norm.telomere.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/kNTRd7dAzQ/norm.telomere.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/kNTRd7dAzQ/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.1.out
+ /<<PKGBUILDDIR>>/test/view.1.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/kNTRd7dAzQ/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.1.out
+ /<<PKGBUILDDIR>>/test/view.1.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/kNTRd7dAzQ/view.vcf.gz -r20,Y
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.2.out
+ /<<PKGBUILDDIR>>/test/view.2.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/kNTRd7dAzQ/view.vcf.gz -r20,Y | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.2.out
+ /<<PKGBUILDDIR>>/test/view.2.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -xs NA00003 /tmp/kNTRd7dAzQ/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.3.out
+ /<<PKGBUILDDIR>>/test/view.3.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -xs NA00003 /tmp/kNTRd7dAzQ/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.3.out
+ /<<PKGBUILDDIR>>/test/view.3.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/kNTRd7dAzQ/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.4.out
+ /<<PKGBUILDDIR>>/test/view.4.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/kNTRd7dAzQ/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.4.out
+ /<<PKGBUILDDIR>>/test/view.4.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -p /tmp/kNTRd7dAzQ/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.5.out
+ /<<PKGBUILDDIR>>/test/view.5.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -p /tmp/kNTRd7dAzQ/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.5.out
+ /<<PKGBUILDDIR>>/test/view.5.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -P /tmp/kNTRd7dAzQ/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.6.out
+ /<<PKGBUILDDIR>>/test/view.6.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -P /tmp/kNTRd7dAzQ/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.6.out
+ /<<PKGBUILDDIR>>/test/view.6.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/kNTRd7dAzQ/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/kNTRd7dAzQ/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -Hu /tmp/kNTRd7dAzQ/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -GVsnps /tmp/kNTRd7dAzQ/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.9.out
+ /<<PKGBUILDDIR>>/test/view.9.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -GVsnps /tmp/kNTRd7dAzQ/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.9.out
+ /<<PKGBUILDDIR>>/test/view.9.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/kNTRd7dAzQ/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.10.out
+ /<<PKGBUILDDIR>>/test/view.10.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/kNTRd7dAzQ/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.10.out
+ /<<PKGBUILDDIR>>/test/view.10.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -s ^NA00003 /tmp/kNTRd7dAzQ/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.exclude.out
+ /<<PKGBUILDDIR>>/test/view.exclude.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -s ^NA00003 /tmp/kNTRd7dAzQ/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.exclude.out
+ /<<PKGBUILDDIR>>/test/view.exclude.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version /tmp/kNTRd7dAzQ/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/view.omitgenotypes.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -G /tmp/kNTRd7dAzQ/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -G /tmp/kNTRd7dAzQ/view.omitgenotypes.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -HG /tmp/kNTRd7dAzQ/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -a /tmp/kNTRd7dAzQ/many.alleles.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -a /tmp/kNTRd7dAzQ/many.alleles.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asA /tmp/kNTRd7dAzQ/view.vectors.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asA /tmp/kNTRd7dAzQ/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asB /tmp/kNTRd7dAzQ/view.vectors.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asB /tmp/kNTRd7dAzQ/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asA /tmp/kNTRd7dAzQ/view.vectors.2.vcf.gz
+[E::bcf_remove_allele_set] Unexpected number of values in INFO/IAF at 1:10; expected Number=A=2, but found 1
+Error: Could not trim alleles at 1:10
+
+ Non-zero status 255
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asA /tmp/kNTRd7dAzQ/view.vectors.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_remove_allele_set] Unexpected number of values in INFO/IAF at 1:10; expected Number=A=2, but found 1
+Error: Could not trim alleles at 1:10
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[0]="AAAAAA"' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[2]="C"' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[4]="EE"' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FRS[1]="BB"' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'TXT0="text"' /tmp/kNTRd7dAzQ/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -T /<<PKGBUILDDIR>>/test/view.chrs.tab /tmp/kNTRd7dAzQ/view.chrs.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -T /<<PKGBUILDDIR>>/test/view.chrs.tab /tmp/kNTRd7dAzQ/view.chrs.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -i 'POS>=3062917' /tmp/kNTRd7dAzQ/filter.2.vcf.gz 1:3062917-3157410
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -i 'POS>=3062917' /tmp/kNTRd7dAzQ/filter.2.vcf.gz 1:3062917-3157410 | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'TXT0="text"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'TXT0="text"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FRS[1]="BB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FRS[1]="BB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[0]="AAAAAA"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[0]="AAAAAA"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[1]="BBB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[1]="BBB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[4]="EE"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[4]="EE"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/STR="XX"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/STR="XX"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -C5:nonmajor /tmp/kNTRd7dAzQ/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -c6:nonmajor /tmp/kNTRd7dAzQ/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -q0.3:major /tmp/kNTRd7dAzQ/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/kNTRd7dAzQ/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/kNTRd7dAzQ/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/kNTRd7dAzQ/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mg0 /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup.2.out
+ /<<PKGBUILDDIR>>/test/mpileup.2.out.new
+.. failed ...
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mg0 /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup.2.out
+ /<<PKGBUILDDIR>>/test/mpileup.2.out.new
+.. failed ...
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call_cAls:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mA -C alleles -T /tmp/kNTRd7dAzQ/mpileup.tab.gz /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call_cAls:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mA -C alleles -T /tmp/kNTRd7dAzQ/mpileup.tab.gz /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv /<<PKGBUILDDIR>>/test/mpileup.c.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv /<<PKGBUILDDIR>>/test/mpileup.c.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -mx -g2 -G2 /<<PKGBUILDDIR>>/test/filter.1.vcf | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/filter.1.out
+ /<<PKGBUILDDIR>>/test/filter.1.out.new
+.. failed ...
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -mx -g2 -G2 /<<PKGBUILDDIR>>/test/filter.1.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/filter.1.out
+ /<<PKGBUILDDIR>>/test/filter.1.out.new
+.. failed ...
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<<PKGBUILDDIR>>/test/filter.2.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'ALT="."' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'ALT="."' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S . -i 'FORMAT/TEST3<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S . -i 'FORMAT/TEST4<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="A"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="A"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="RR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="RR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="RA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="RA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="AR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="AR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="AA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="AA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="aA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="aA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="Aa"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="Aa"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HOM"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HOM"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HET"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HET"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HAP"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HAP"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -m 0 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.VY4puM
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -Ob -m 0 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.3MuDN8
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -m 1000 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.1CuKKi
+Merging 4 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -Ob -m 1000 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.Mu5b9q
+Merging 4 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<<PKGBUILDDIR>>/test/regions.tab /tmp/kNTRd7dAzQ/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<<PKGBUILDDIR>>/test/regions.tab
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /<<PKGBUILDDIR>>/test/regions.tab /tmp/kNTRd7dAzQ/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/kNTRd7dAzQ/regions.tab.gz /tmp/kNTRd7dAzQ/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/kNTRd7dAzQ/regions.tab.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/kNTRd7dAzQ/regions.tab.gz /tmp/kNTRd7dAzQ/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/kNTRd7dAzQ/regions.bed /tmp/kNTRd7dAzQ/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/kNTRd7dAzQ/regions.bed
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/kNTRd7dAzQ/regions.bed /tmp/kNTRd7dAzQ/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/kNTRd7dAzQ/regions.bed.gz /tmp/kNTRd7dAzQ/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/kNTRd7dAzQ/regions.bed.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/kNTRd7dAzQ/regions.bed.gz /tmp/kNTRd7dAzQ/regions.vcf.gz
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/kNTRd7dAzQ/annotate.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/kNTRd7dAzQ/annotate.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/kNTRd7dAzQ/annotate2.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/kNTRd7dAzQ/annotate2.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/kNTRd7dAzQ/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/kNTRd7dAzQ/annotate.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/kNTRd7dAzQ/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/kNTRd7dAzQ/annotate.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/kNTRd7dAzQ/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/kNTRd7dAzQ/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/kNTRd7dAzQ/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/kNTRd7dAzQ/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/kNTRd7dAzQ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/kNTRd7dAzQ/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/kNTRd7dAzQ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/kNTRd7dAzQ/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -x FORMAT /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -x FORMAT /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/kNTRd7dAzQ/annots4.vcf.gz -c +INFO /tmp/kNTRd7dAzQ/annotate4.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/kNTRd7dAzQ/annots4.vcf.gz -c +INFO /tmp/kNTRd7dAzQ/annotate4.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/kNTRd7dAzQ/annots4.tab.gz -h /<<PKGBUILDDIR>>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<<PKGBUILDDIR>>/test/annotate4.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/kNTRd7dAzQ/annots4.tab.gz -h /<<PKGBUILDDIR>>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<<PKGBUILDDIR>>/test/annotate4.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/kNTRd7dAzQ/annots10.tab.gz -h /<<PKGBUILDDIR>>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<<PKGBUILDDIR>>/test/annotate10.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/kNTRd7dAzQ/annots10.tab.gz -h /<<PKGBUILDDIR>>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<<PKGBUILDDIR>>/test/annotate10.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/kNTRd7dAzQ/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/kNTRd7dAzQ/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/kNTRd7dAzQ/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/kNTRd7dAzQ/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/kNTRd7dAzQ/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<<PKGBUILDDIR>>/test/annotate2.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/kNTRd7dAzQ/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<<PKGBUILDDIR>>/test/annotate2.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/kNTRd7dAzQ/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/kNTRd7dAzQ/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/kNTRd7dAzQ/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/kNTRd7dAzQ/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/kNTRd7dAzQ/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/kNTRd7dAzQ/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/kNTRd7dAzQ/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/kNTRd7dAzQ/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +missing2ref --no-version /tmp/kNTRd7dAzQ/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +missing2ref --no-version /tmp/kNTRd7dAzQ/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/kNTRd7dAzQ/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/kNTRd7dAzQ/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/kNTRd7dAzQ/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/kNTRd7dAzQ/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/kNTRd7dAzQ/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<<PKGBUILDDIR>>/test/annotate9.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/kNTRd7dAzQ/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<<PKGBUILDDIR>>/test/annotate9.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-AN-AC --no-version /tmp/kNTRd7dAzQ/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-AN-AC --no-version /tmp/kNTRd7dAzQ/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +dosage /tmp/kNTRd7dAzQ/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +dosage /tmp/kNTRd7dAzQ/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixploidy --no-version /tmp/kNTRd7dAzQ/fixploidy.vcf.gz -- -s /<<PKGBUILDDIR>>/test/fixploidy.samples -p /<<PKGBUILDDIR>>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixploidy --no-version /tmp/kNTRd7dAzQ/fixploidy.bcf -- -s /<<PKGBUILDDIR>>/test/fixploidy.samples -p /<<PKGBUILDDIR>>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/kNTRd7dAzQ/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/kNTRd7dAzQ/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/kNTRd7dAzQ/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/kNTRd7dAzQ/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/kNTRd7dAzQ/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/kNTRd7dAzQ/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/kNTRd7dAzQ/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/kNTRd7dAzQ/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/kNTRd7dAzQ/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/kNTRd7dAzQ/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/kNTRd7dAzQ/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/kNTRd7dAzQ/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/kNTRd7dAzQ/view.vcf.gz -- -t AC -S /<<PKGBUILDDIR>>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/kNTRd7dAzQ/view.bcf -- -t AC -S /<<PKGBUILDDIR>>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/kNTRd7dAzQ/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/kNTRd7dAzQ/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/kNTRd7dAzQ/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/kNTRd7dAzQ/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/kNTRd7dAzQ/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +trio-switch-rate /tmp/kNTRd7dAzQ/trio.vcf.gz -- -p /<<PKGBUILDDIR>>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +trio-switch-rate /tmp/kNTRd7dAzQ/trio.bcf -- -p /<<PKGBUILDDIR>>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +ad-bias /tmp/kNTRd7dAzQ/ad-bias.vcf.gz -- -s /<<PKGBUILDDIR>>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +ad-bias /tmp/kNTRd7dAzQ/ad-bias.bcf -- -s /<<PKGBUILDDIR>>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +af-dist /tmp/kNTRd7dAzQ/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +af-dist /tmp/kNTRd7dAzQ/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixref /tmp/kNTRd7dAzQ/fixref.2a.vcf.gz -- -f /<<PKGBUILDDIR>>/test/norm.fa -i /tmp/kNTRd7dAzQ/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixref /tmp/kNTRd7dAzQ/fixref.2a.bcf -- -f /<<PKGBUILDDIR>>/test/norm.fa -i /tmp/kNTRd7dAzQ/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/kNTRd7dAzQ/aa.vcf.gz -- -f /<<PKGBUILDDIR>>/test/aa.fa -c AA -h /<<PKGBUILDDIR>>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/aa.out
+ /<<PKGBUILDDIR>>/test/aa.out.new
+.. failed ...
+
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/kNTRd7dAzQ/aa.bcf -- -f /<<PKGBUILDDIR>>/test/aa.fa -c AA -h /<<PKGBUILDDIR>>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/aa.out
+ /<<PKGBUILDDIR>>/test/aa.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/kNTRd7dAzQ/ref.vcf.gz -- -f /<<PKGBUILDDIR>>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+
+ Non-zero status 1
+.. failed ...
+
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/kNTRd7dAzQ/ref.bcf -- -f /<<PKGBUILDDIR>>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/ref.out
+ /<<PKGBUILDDIR>>/test/ref.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/kNTRd7dAzQ/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/kNTRd7dAzQ/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/kNTRd7dAzQ/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/kNTRd7dAzQ/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/kNTRd7dAzQ/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/kNTRd7dAzQ/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/kNTRd7dAzQ/mendelian.vcf.gz -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/kNTRd7dAzQ/mendelian.bcf -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/kNTRd7dAzQ/mendelian.vcf.gz -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/kNTRd7dAzQ/mendelian.bcf -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/kNTRd7dAzQ/mendelian.vcf.gz -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/kNTRd7dAzQ/mendelian.bcf -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version /tmp/kNTRd7dAzQ/concat.1.a.vcf.gz /tmp/kNTRd7dAzQ/concat.1.b.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob /tmp/kNTRd7dAzQ/concat.1.a.vcf.gz /tmp/kNTRd7dAzQ/concat.1.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.1.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.1.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version /tmp/kNTRd7dAzQ/concat.1.a.bcf /tmp/kNTRd7dAzQ/concat.1.b.bcf
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob /tmp/kNTRd7dAzQ/concat.1.a.bcf /tmp/kNTRd7dAzQ/concat.1.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -a /tmp/kNTRd7dAzQ/concat.2.a.vcf.gz /tmp/kNTRd7dAzQ/concat.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -a /tmp/kNTRd7dAzQ/concat.2.a.vcf.gz /tmp/kNTRd7dAzQ/concat.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -a /tmp/kNTRd7dAzQ/concat.2.a.bcf /tmp/kNTRd7dAzQ/concat.2.b.bcf
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -a /tmp/kNTRd7dAzQ/concat.2.a.bcf /tmp/kNTRd7dAzQ/concat.2.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -aD /tmp/kNTRd7dAzQ/concat.2.a.vcf.gz /tmp/kNTRd7dAzQ/concat.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -aD /tmp/kNTRd7dAzQ/concat.2.a.vcf.gz /tmp/kNTRd7dAzQ/concat.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -aD /tmp/kNTRd7dAzQ/concat.2.a.bcf /tmp/kNTRd7dAzQ/concat.2.b.bcf
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -aD /tmp/kNTRd7dAzQ/concat.2.a.bcf /tmp/kNTRd7dAzQ/concat.2.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -l /tmp/kNTRd7dAzQ/concat.3.a.vcf.gz /tmp/kNTRd7dAzQ/concat.3.b.vcf.gz /tmp/kNTRd7dAzQ/concat.3.0.vcf.gz /tmp/kNTRd7dAzQ/concat.3.c.vcf.gz /tmp/kNTRd7dAzQ/concat.3.d.vcf.gz /tmp/kNTRd7dAzQ/concat.3.e.vcf.gz /tmp/kNTRd7dAzQ/concat.3.f.vcf.gz
+[E::vcf_format] Invalid BCF, the FORMAT tag id=-13056 not present in the header
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -l /tmp/kNTRd7dAzQ/concat.3.a.vcf.gz /tmp/kNTRd7dAzQ/concat.3.b.vcf.gz /tmp/kNTRd7dAzQ/concat.3.0.vcf.gz /tmp/kNTRd7dAzQ/concat.3.c.vcf.gz /tmp/kNTRd7dAzQ/concat.3.d.vcf.gz /tmp/kNTRd7dAzQ/concat.3.e.vcf.gz /tmp/kNTRd7dAzQ/concat.3.f.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+GT is not present at 2:280. (This warning is printed only once.)
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -13056
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out.new
+.. failed ...
+
+[W::bcf_record_check] Bad BCF record: Invalid INFO id -14336
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -l /tmp/kNTRd7dAzQ/concat.3.a.bcf /tmp/kNTRd7dAzQ/concat.3.b.bcf /tmp/kNTRd7dAzQ/concat.3.0.bcf /tmp/kNTRd7dAzQ/concat.3.c.bcf /tmp/kNTRd7dAzQ/concat.3.d.bcf /tmp/kNTRd7dAzQ/concat.3.e.bcf /tmp/kNTRd7dAzQ/concat.3.f.bcf
+[W::bcf_record_check] Bad BCF record: Invalid INFO id -14336
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080
+[E::vcf_format] Invalid BCF, the FORMAT tag id=-13056 not present in the header
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -l /tmp/kNTRd7dAzQ/concat.3.a.bcf /tmp/kNTRd7dAzQ/concat.3.b.bcf /tmp/kNTRd7dAzQ/concat.3.0.bcf /tmp/kNTRd7dAzQ/concat.3.c.bcf /tmp/kNTRd7dAzQ/concat.3.d.bcf /tmp/kNTRd7dAzQ/concat.3.e.bcf /tmp/kNTRd7dAzQ/concat.3.f.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[W::bcf_record_check] Bad BCF record: Invalid INFO id -14336
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -13056
+Random seed for test_naive_concat: 2218402585
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out.new
+.. failed ...
+
+test_naive_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --naive /tmp/kNTRd7dAzQ/naive_concat.0.bcf /tmp/kNTRd7dAzQ/naive_concat.1.bcf /tmp/kNTRd7dAzQ/naive_concat.2.bcf /tmp/kNTRd7dAzQ/naive_concat.3.bcf /tmp/kNTRd7dAzQ/naive_concat.4.bcf /tmp/kNTRd7dAzQ/naive_concat.5.bcf /tmp/kNTRd7dAzQ/naive_concat.6.bcf /tmp/kNTRd7dAzQ/naive_concat.7.bcf /tmp/kNTRd7dAzQ/naive_concat.8.bcf /tmp/kNTRd7dAzQ/naive_concat.9.bcf | /<<PKGBUILDDIR>>/bcftools view -H
+[E::hts_realloc_or_die] Cannot allocate memory
+Failed to open -: unknown file type
+
+ Non-zero status 255
+.. failed ...
+
+test_naive_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --naive /tmp/kNTRd7dAzQ/naive_concat.0.vcf.gz /tmp/kNTRd7dAzQ/naive_concat.1.vcf.gz /tmp/kNTRd7dAzQ/naive_concat.2.vcf.gz /tmp/kNTRd7dAzQ/naive_concat.3.vcf.gz /tmp/kNTRd7dAzQ/naive_concat.4.vcf.gz /tmp/kNTRd7dAzQ/naive_concat.5.vcf.gz /tmp/kNTRd7dAzQ/naive_concat.6.vcf.gz /tmp/kNTRd7dAzQ/naive_concat.7.vcf.gz /tmp/kNTRd7dAzQ/naive_concat.8.vcf.gz /tmp/kNTRd7dAzQ/naive_concat.9.vcf.gz | /<<PKGBUILDDIR>>/bcftools view -H
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.naive.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.naive.vcf.out.new
+.. failed ...
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /tmp/kNTRd7dAzQ/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/kNTRd7dAzQ/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /tmp/kNTRd7dAzQ/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/kNTRd7dAzQ/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /tmp/kNTRd7dAzQ/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/kNTRd7dAzQ/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /tmp/kNTRd7dAzQ/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/kNTRd7dAzQ/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /tmp/kNTRd7dAzQ/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/kNTRd7dAzQ/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /tmp/kNTRd7dAzQ/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/kNTRd7dAzQ/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /tmp/kNTRd7dAzQ/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/kNTRd7dAzQ/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /tmp/kNTRd7dAzQ/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/kNTRd7dAzQ/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /tmp/kNTRd7dAzQ/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/kNTRd7dAzQ/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /tmp/kNTRd7dAzQ/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/kNTRd7dAzQ/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /<<PKGBUILDDIR>>/test/empty.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/empty.vcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /tmp/kNTRd7dAzQ/empty.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/kNTRd7dAzQ/empty.bcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /tmp/kNTRd7dAzQ/empty.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/kNTRd7dAzQ/empty.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/kNTRd7dAzQ/rename.map -Ov /tmp/kNTRd7dAzQ/annotate.bcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/kNTRd7dAzQ/rename.map -Ob /tmp/kNTRd7dAzQ/annotate.bcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/kNTRd7dAzQ/rename.map -Ov /<<PKGBUILDDIR>>/test/annotate.vcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/kNTRd7dAzQ/rename.map -Ob /<<PKGBUILDDIR>>/test/annotate.vcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. /tmp/kNTRd7dAzQ/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- /tmp/kNTRd7dAzQ/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --tag PL /tmp/kNTRd7dAzQ/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --tag PL /tmp/kNTRd7dAzQ/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --vcf-ids /tmp/kNTRd7dAzQ/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --vcf-ids /tmp/kNTRd7dAzQ/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom /tmp/kNTRd7dAzQ/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom /tmp/kNTRd7dAzQ/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom --vcf-ids /tmp/kNTRd7dAzQ/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom --vcf-ids /tmp/kNTRd7dAzQ/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h -,.,. /tmp/kNTRd7dAzQ/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h -,.,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h .,-,. /tmp/kNTRd7dAzQ/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h .,-,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h .,.,- /tmp/kNTRd7dAzQ/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h .,.,- 2>/dev/null
+.. ok
+
+test_vcf_convert_hls2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -H /<<PKGBUILDDIR>>/test/convert.hls.gt.hap,/<<PKGBUILDDIR>>/test/convert.hls.gt.legend,/<<PKGBUILDDIR>>/test/convert.hls.gt.samples 2>/dev/null | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert_hls2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -H /<<PKGBUILDDIR>>/test/convert.hls.gt.hap,/<<PKGBUILDDIR>>/test/convert.hls.gt.legend,/<<PKGBUILDDIR>>/test/convert.hls.gt.samples -Ou 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert_hs2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample2vcf /<<PKGBUILDDIR>>/test/convert.hs.gt.hap,/<<PKGBUILDDIR>>/test/convert.hs.gt.samples 2>/dev/null | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert_hs2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample2vcf /<<PKGBUILDDIR>>/test/convert.hs.gt.hap,/<<PKGBUILDDIR>>/test/convert.hs.gt.samples -Ou 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample -,. /tmp/kNTRd7dAzQ/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --hapsample -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample .,- /tmp/kNTRd7dAzQ/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --hapsample .,- 2>/dev/null
+.. ok
+
+test_vcf_convert_gvcf:
+ /<<PKGBUILDDIR>>/bcftools convert --no-version --gvcf2vcf -f /<<PKGBUILDDIR>>/test/gvcf.fa /tmp/kNTRd7dAzQ/convert.gvcf.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out.new
+.. failed ...
+
+test_vcf_convert_gvcf:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/kNTRd7dAzQ/convert.gvcf.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --gvcf2vcf -f /<<PKGBUILDDIR>>/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out.new
+.. failed ...
+
+test_vcf_convert_tsv2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /<<PKGBUILDDIR>>/test/23andme.fa --tsv2vcf /<<PKGBUILDDIR>>/test/convert.23andme 2>/dev/null
+.. ok
+
+test_vcf_convert_tsv2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /<<PKGBUILDDIR>>/test/23andme.fa --tsv2vcf /<<PKGBUILDDIR>>/test/convert.23andme 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/kNTRd7dAzQ/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/kNTRd7dAzQ/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/kNTRd7dAzQ/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/kNTRd7dAzQ/consensus.1.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/kNTRd7dAzQ/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/kNTRd7dAzQ/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/kNTRd7dAzQ/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/kNTRd7dAzQ/consensus.2.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/kNTRd7dAzQ/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -I -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/kNTRd7dAzQ/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -I -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/kNTRd7dAzQ/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/kNTRd7dAzQ/consensus.3.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/kNTRd7dAzQ/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/kNTRd7dAzQ/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -c /tmp/kNTRd7dAzQ/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/kNTRd7dAzQ/consensus.4.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/kNTRd7dAzQ/consensus2.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus2.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/kNTRd7dAzQ/consensus2.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus2.fa -H 2 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/kNTRd7dAzQ/empty.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa 2>/dev/null
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -b /tmp/kNTRd7dAzQ/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/kNTRd7dAzQ/mpileup.bam.urllist 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -b /tmp/kNTRd7dAzQ/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/kNTRd7dAzQ/mpileup.cram.urllist 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_csq:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq.fa -g /<<PKGBUILDDIR>>/test/csq.gff3 /<<PKGBUILDDIR>>/test/csq.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq.gff3 ...
+Indexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq.1.out
+ /<<PKGBUILDDIR>>/test/csq.1.out.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff /<<PKGBUILDDIR>>/test/csq/ENST00000373833/boundary-insertion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff /<<PKGBUILDDIR>>/test/csq/ENST00000373833/boundary-insertion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff /<<PKGBUILDDIR>>/test/csq/ENST00000318249/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff /<<PKGBUILDDIR>>/test/csq/ENST00000318249/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff /<<PKGBUILDDIR>>/test/csq/ENST00000303039/not-a-stop.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff /<<PKGBUILDDIR>>/test/csq/ENST00000303039/not-a-stop.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520795/long-inside-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520795/long-inside-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.gff /<<PKGBUILDDIR>>/test/csq/ENST00000357367/stop-retained.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.gff ...
+Indexed 1 transcripts, 4 exons, 3 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.gff /<<PKGBUILDDIR>>/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.gff ...
+Indexed 1 transcripts, 26 exons, 26 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff /<<PKGBUILDDIR>>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff /<<PKGBUILDDIR>>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.gff /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.gff ...
+Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.gff /<<PKGBUILDDIR>>/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff /<<PKGBUILDDIR>>/test/csq/ENST00000329454/boundary-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff /<<PKGBUILDDIR>>/test/csq/ENST00000329454/boundary-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.gff /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 2 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.gff /<<PKGBUILDDIR>>/test/csq/ENST00000519442/synon-splice-region-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.gff /<<PKGBUILDDIR>>/test/csq/ENST00000256452/intron.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.gff ...
+Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff /<<PKGBUILDDIR>>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff /<<PKGBUILDDIR>>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.gff /<<PKGBUILDDIR>>/test/csq/ENST00000420670/start-stop-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.gff ...
+Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.gff /<<PKGBUILDDIR>>/test/csq/ENST00000593942/last-codon-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.gff ...
+Indexed 1 transcripts, 7 exons, 4 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.gff /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff /<<PKGBUILDDIR>>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff /<<PKGBUILDDIR>>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.gff /<<PKGBUILDDIR>>/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.gff /<<PKGBUILDDIR>>/test/csq/ENST00000409523/long-overlapping-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff /<<PKGBUILDDIR>>/test/csq/ENST00000542803/splice-region.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff /<<PKGBUILDDIR>>/test/csq/ENST00000542803/splice-region.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ambiguous.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ambiguous.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ambiguous.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff /<<PKGBUILDDIR>>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff /<<PKGBUILDDIR>>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.fa -g /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.gff /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/synon.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.gff ...
+Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff /<<PKGBUILDDIR>>/test/csq/ENST00000218032/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff /<<PKGBUILDDIR>>/test/csq/ENST00000218032/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.gff /<<PKGBUILDDIR>>/test/csq/ENST00000381157/haploid-diploid.vcf | /<<PKGBUILDDIR>>/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 0 UTRs
+Calling...
+Warning: Skipping site with non-diploid/non-haploid genotypes at X:31180 C>T
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000381157/haploid-diploid.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000381157/haploid-diploid.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.gff /<<PKGBUILDDIR>>/test/csq/ENST00000413103/long-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.gff ...
+Indexed 1 transcripts, 2 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.gff /<<PKGBUILDDIR>>/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.gff /<<PKGBUILDDIR>>/test/csq/ENST00000436063/insert-before-utr.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.gff ...
+Indexed 1 transcripts, 7 exons, 7 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.gff /<<PKGBUILDDIR>>/test/csq/ENST00000557788/long-overlap-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff /<<PKGBUILDDIR>>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff /<<PKGBUILDDIR>>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.gff /<<PKGBUILDDIR>>/test/csq/ENST00000390520/deletion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff /<<PKGBUILDDIR>>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff /<<PKGBUILDDIR>>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.gff /<<PKGBUILDDIR>>/test/csq/ENST00000545279/splice-region-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.gff ...
+Indexed 1 transcripts, 9 exons, 7 CDSs, 4 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.gff /<<PKGBUILDDIR>>/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.gff ...
+Indexed 1 transcripts, 7 exons, 6 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520868/long-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/snps.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/snps.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/insert3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/insert3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+
+Number of tests:
+ total .. 728
+ passed .. 607
+ failed .. 121
+
+Makefile:246: recipe for target 'test-plugins' failed
+make[1]: *** [test-plugins] Error 1
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+dh_auto_test: make -j16 test VERBOSE=1 returned exit code 2
+debian/rules:7: recipe for target 'build-arch' failed
+make: *** [build-arch] Error 2
+dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
+--------------------------------------------------------------------------------
+Build finished at 2017-12-11T16:43:20Z
+
+Finished
+--------
+
+
++------------------------------------------------------------------------------+
+| Cleanup |
++------------------------------------------------------------------------------+
+
+Purging /<<BUILDDIR>>
+Not cleaning session: cloned chroot in use
+E: Build failure (dpkg-buildpackage died)
+
++------------------------------------------------------------------------------+
+| Summary |
++------------------------------------------------------------------------------+
+
+Build Architecture: ppc64
+Build Type: any
+Build-Space: 30500
+Build-Time: 48
+Distribution: experimental
+Fail-Stage: build
+Host Architecture: ppc64
+Install-Time: 46
+Job: bcftools_1.6-1
+Machine Architecture: ppc64
+Package: bcftools
+Package-Time: 114
+Source-Version: 1.6-1
+Space: 30500
+Status: attempted
+Version: 1.6-1
+--------------------------------------------------------------------------------
+Finished at 2017-12-11T16:43:20Z
+Build needed 00:01:54, 30500k disk space
diff --git a/bcftools_1.6-1_s390x.log b/bcftools_1.6-1_s390x.log
new file mode 100644
index 0000000..8153699
--- /dev/null
+++ b/bcftools_1.6-1_s390x.log
@@ -0,0 +1,4530 @@
+
+sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on zemlinsky.debian.org
+
++==============================================================================+
+| bcftools 1.6-1 (s390x) Mon, 11 Dec 2017 16:05:14 +0000 |
++==============================================================================+
+
+Package: bcftools
+Version: 1.6-1
+Source Version: 1.6-1
+Distribution: experimental
+Machine Architecture: s390x
+Host Architecture: s390x
+Build Architecture: s390x
+Build Type: any
+
+I: NOTICE: Log filtering will replace 'var/run/schroot/mount/experimental-s390x-sbuild-5991431c-cb8c-4fb6-9191-caea4f6f287f' with '<<CHROOT>>'
+
++------------------------------------------------------------------------------+
+| Update chroot |
++------------------------------------------------------------------------------+
+
+Get:1 http://ftp.debian.org/debian unstable InRelease [240 kB]
+Get:2 http://ftp.debian.org/debian experimental InRelease [107 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian unstable InRelease [240 kB]
+Get:4 http://ftp-stud.hs-esslingen.de/debian experimental InRelease [107 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:6 http://ftp.debian.org/debian unstable/main Sources [7953 kB]
+Get:7 http://ftp.debian.org/debian unstable/non-free Sources [83.9 kB]
+Get:8 http://ftp.debian.org/debian unstable/contrib Sources [50.5 kB]
+Get:9 http://ftp.debian.org/debian unstable/contrib s390x Packages [45.1 kB]
+Get:10 http://ftp.debian.org/debian unstable/main s390x Packages [7522 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian unstable/non-free Sources [83.9 kB]
+Get:12 http://ftp-stud.hs-esslingen.de/debian unstable/main Sources [7953 kB]
+Get:13 http://incoming.debian.org/debian-buildd buildd-experimental InRelease [58.9 kB]
+Get:14 http://ftp.debian.org/debian experimental/non-free Sources [3012 B]
+Get:15 http://ftp.debian.org/debian experimental/main Sources [262 kB]
+Get:16 http://ftp.debian.org/debian experimental/contrib Sources [1692 B]
+Get:17 http://ftp.debian.org/debian experimental/main s390x Packages [374 kB]
+Get:18 http://ftp.debian.org/debian experimental/contrib s390x Packages [1564 B]
+Get:19 http://ftp-stud.hs-esslingen.de/debian unstable/contrib Sources [50.5 kB]
+Get:20 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x Packages [7521 kB]
+Get:21 http://ftp-stud.hs-esslingen.de/debian unstable/contrib s390x Packages [45.1 kB]
+Get:22 http://ftp-stud.hs-esslingen.de/debian experimental/main Sources [263 kB]
+Get:23 http://ftp-stud.hs-esslingen.de/debian experimental/contrib Sources [1692 B]
+Get:24 http://ftp-stud.hs-esslingen.de/debian experimental/non-free Sources [3012 B]
+Get:25 http://ftp-stud.hs-esslingen.de/debian experimental/contrib s390x Packages [1564 B]
+Get:26 http://ftp-stud.hs-esslingen.de/debian experimental/main s390x Packages [375 kB]
+Get:27 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [123 kB]
+Get:28 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1916 B]
+Get:29 http://incoming.debian.org/debian-buildd buildd-unstable/contrib s390x Packages [1468 B]
+Get:30 http://incoming.debian.org/debian-buildd buildd-unstable/main s390x Packages [132 kB]
+Get:31 http://incoming.debian.org/debian-buildd buildd-experimental/main Sources [30.7 kB]
+Get:32 http://incoming.debian.org/debian-buildd buildd-experimental/main s390x Packages [56.7 kB]
+Fetched 33.8 MB in 10s (3194 kB/s)
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Fetch source files |
++------------------------------------------------------------------------------+
+
+
+Check APT
+---------
+
+Checking available source versions...
+
+Download source files with APT
+------------------------------
+
+Reading package lists...
+NOTICE: 'bcftools' packaging is maintained in the 'Git' version control system at:
+https://anonscm.debian.org/git/debian-med/bcftools.git
+Please use:
+git clone https://anonscm.debian.org/git/debian-med/bcftools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 2342 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (dsc) [2110 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (tar) [2333 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (diff) [6088 B]
+Fetched 2342 kB in 1s (1397 kB/s)
+Download complete and in download only mode
+I: NOTICE: Log filtering will replace 'build/bcftools-ujuKNt/bcftools-1.6' with '<<PKGBUILDDIR>>'
+I: NOTICE: Log filtering will replace 'build/bcftools-ujuKNt' with '<<BUILDDIR>>'
+
++------------------------------------------------------------------------------+
+| 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 '/<<BUILDDIR>>/resolver-TsccH3/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:/<<BUILDDIR>>/resolver-TsccH3/apt_archive ./ InRelease
+Get:2 copy:/<<BUILDDIR>>/resolver-TsccH3/apt_archive ./ Release [957 B]
+Ign:3 copy:/<<BUILDDIR>>/resolver-TsccH3/apt_archive ./ Release.gpg
+Get:4 copy:/<<BUILDDIR>>/resolver-TsccH3/apt_archive ./ Sources [349 B]
+Get:5 copy:/<<BUILDDIR>>/resolver-TsccH3/apt_archive ./ Packages [432 B]
+Fetched 1738 B in 0s (62.1 kB/s)
+Reading package lists...
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Install core build dependencies (aptitude-based resolver) |
++------------------------------------------------------------------------------+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following additional packages will be installed:
+ aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+Suggested packages:
+ aptitude-doc-en | aptitude-doc apt-xapian-index debtags tasksel
+ libcwidget-dev xapian-tools
+Recommended packages:
+ libparse-debianchangelog-perl
+The following NEW packages will be installed:
+ aptitude aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+0 upgraded, 9 newly installed, 0 to remove and 2 not upgraded.
+Need to get 5001 kB of archives.
+After this operation, 20.6 MB of additional disk space will be used.
+Get:1 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libxapian30 s390x 1.4.5-1 [1019 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libsqlite3-0 s390x 3.21.0-1 [561 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x aptitude-common all 0.8.10-1 [1591 kB]
+Get:4 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libboost-system1.62.0 s390x 1.62.0+dfsg-4+b2 [32.7 kB]
+Get:5 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libboost-filesystem1.62.0 s390x 1.62.0+dfsg-4+b2 [61.4 kB]
+Get:6 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libboost-iostreams1.62.0 s390x 1.62.0+dfsg-4+b2 [50.8 kB]
+Get:7 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libsigc++-2.0-0v5 s390x 2.10.0-1 [61.2 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libcwidget3v5 s390x 0.5.17-6 [280 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x aptitude s390x 0.8.10-1 [1343 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 5001 kB in 0s (15.9 MB/s)
+Selecting previously unselected package libxapian30:s390x.
+(Reading database ... 11465 files and directories currently installed.)
+Preparing to unpack .../0-libxapian30_1.4.5-1_s390x.deb ...
+Unpacking libxapian30:s390x (1.4.5-1) ...
+Selecting previously unselected package libsqlite3-0:s390x.
+Preparing to unpack .../1-libsqlite3-0_3.21.0-1_s390x.deb ...
+Unpacking libsqlite3-0:s390x (3.21.0-1) ...
+Selecting previously unselected package aptitude-common.
+Preparing to unpack .../2-aptitude-common_0.8.10-1_all.deb ...
+Unpacking aptitude-common (0.8.10-1) ...
+Selecting previously unselected package libboost-system1.62.0:s390x.
+Preparing to unpack .../3-libboost-system1.62.0_1.62.0+dfsg-4+b2_s390x.deb ...
+Unpacking libboost-system1.62.0:s390x (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libboost-filesystem1.62.0:s390x.
+Preparing to unpack .../4-libboost-filesystem1.62.0_1.62.0+dfsg-4+b2_s390x.deb ...
+Unpacking libboost-filesystem1.62.0:s390x (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libboost-iostreams1.62.0:s390x.
+Preparing to unpack .../5-libboost-iostreams1.62.0_1.62.0+dfsg-4+b2_s390x.deb ...
+Unpacking libboost-iostreams1.62.0:s390x (1.62.0+dfsg-4+b2) ...
+Selecting previously unselected package libsigc++-2.0-0v5:s390x.
+Preparing to unpack .../6-libsigc++-2.0-0v5_2.10.0-1_s390x.deb ...
+Unpacking libsigc++-2.0-0v5:s390x (2.10.0-1) ...
+Selecting previously unselected package libcwidget3v5:s390x.
+Preparing to unpack .../7-libcwidget3v5_0.5.17-6_s390x.deb ...
+Unpacking libcwidget3v5:s390x (0.5.17-6) ...
+Selecting previously unselected package aptitude.
+Preparing to unpack .../8-aptitude_0.8.10-1_s390x.deb ...
+Unpacking aptitude (0.8.10-1) ...
+Setting up libxapian30:s390x (1.4.5-1) ...
+Setting up aptitude-common (0.8.10-1) ...
+Setting up libboost-iostreams1.62.0:s390x (1.62.0+dfsg-4+b2) ...
+Processing triggers for libc-bin (2.25-3) ...
+Setting up libsqlite3-0:s390x (3.21.0-1) ...
+Setting up libsigc++-2.0-0v5:s390x (2.10.0-1) ...
+Setting up libboost-system1.62.0:s390x (1.62.0+dfsg-4+b2) ...
+Setting up libboost-filesystem1.62.0:s390x (1.62.0+dfsg-4+b2) ...
+Setting up libcwidget3v5:s390x (0.5.17-6) ...
+Setting up aptitude (0.8.10-1) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode
+Processing triggers for libc-bin (2.25-3) ...
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-core-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-core-dummy:s390x
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+0 packages upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
+Need to get 852 B of archives. After unpacking 0 B will be used.
+Writing extended state information...
+Get: 1 copy:/<<BUILDDIR>>/resolver-TsccH3/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
+Fetched 852 B in 0s (0 B/s)
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11719 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+
++------------------------------------------------------------------------------+
+| Check architectures |
++------------------------------------------------------------------------------+
+
+Arch check ok (s390x included in any)
+
++------------------------------------------------------------------------------+
+| Install package build dependencies |
++------------------------------------------------------------------------------+
+
+
+Setup apt archive
+-----------------
+
+Merged Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+Filtered Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<<BUILDDIR>>/resolver-TsccH3/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:/<<BUILDDIR>>/resolver-TsccH3/apt_archive ./ InRelease
+Get:2 copy:/<<BUILDDIR>>/resolver-TsccH3/apt_archive ./ Release [963 B]
+Ign:3 copy:/<<BUILDDIR>>/resolver-TsccH3/apt_archive ./ Release.gpg
+Get:4 copy:/<<BUILDDIR>>/resolver-TsccH3/apt_archive ./ Sources [546 B]
+Get:5 copy:/<<BUILDDIR>>/resolver-TsccH3/apt_archive ./ Packages [618 B]
+Fetched 2127 B in 0s (76.1 kB/s)
+Reading package lists...
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Install bcftools build dependencies (aptitude-based resolver) |
++------------------------------------------------------------------------------+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+aptitude is already the newest version (0.8.10-1).
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-bcftools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-bcftool [...]
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libbz2-dev{a} libcroco3{a} libcurl3-gnutls{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu57{a} libio-pty-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} l [...]
+The following packages are RECOMMENDED but will NOT be installed:
+ bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules publicsuffix shared-mime-info wget xdg-user-dirs
+0 packages upgraded, 56 newly installed, 0 to remove and 2 not upgraded.
+Need to get 25.3 MB of archives. After unpacking 91.0 MB will be used.
+Writing extended state information...
+Get: 1 copy:/<<BUILDDIR>>/resolver-TsccH3/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [908 B]
+Get: 2 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x groff-base s390x 1.22.3-9 [1213 kB]
+Get: 3 http://ftp.debian.org/debian unstable/main s390x libhts2 s390x 1.5-6 [284 kB]
+Get: 4 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libbsd0 s390x 0.8.6-3 [91.7 kB]
+Get: 5 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libncurses5 s390x 6.0+20171125-1 [92.2 kB]
+Get: 6 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x bsdmainutils s390x 9.0.14 [187 kB]
+Get: 7 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libpipeline1 s390x 1.5.0-1 [28.2 kB]
+Get: 8 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x man-db s390x 2.7.6.1-4 [1036 kB]
+Get: 9 http://ftp.debian.org/debian unstable/main s390x tabix s390x 1.5-6 [296 kB]
+Get: 10 http://ftp.debian.org/debian unstable/main s390x libhts-dev s390x 1.5-6 [362 kB]
+Get: 11 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libssl1.1 s390x 1.1.0g-2 [1041 kB]
+Get: 12 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libmagic-mgc s390x 1:5.32-1 [226 kB]
+Get: 13 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libmagic1 s390x 1:5.32-1 [110 kB]
+Get: 14 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x file s390x 1:5.32-1 [64.3 kB]
+Get: 15 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x gettext-base s390x 0.19.8.1-4 [120 kB]
+Get: 16 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libkeyutils1 s390x 1.5.9-9.2 [12.7 kB]
+Get: 17 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libkrb5support0 s390x 1.15.2-2 [62.2 kB]
+Get: 18 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libk5crypto3 s390x 1.15.2-2 [135 kB]
+Get: 19 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libkrb5-3 s390x 1.15.2-2 [302 kB]
+Get: 20 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libgssapi-krb5-2 s390x 1.15.2-2 [148 kB]
+Get: 21 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libsasl2-modules-db s390x 2.1.27~101-g0780600+dfsg-3 [68.0 kB]
+Get: 22 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libsasl2-2 s390x 2.1.27~101-g0780600+dfsg-3 [103 kB]
+Get: 23 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libldap-common all 2.4.45+dfsg-1 [87.0 kB]
+Get: 24 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libldap-2.4-2 s390x 2.4.45+dfsg-1 [214 kB]
+Get: 25 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libicu57 s390x 57.1-8 [7514 kB]
+Get: 26 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libxml2 s390x 2.9.4+dfsg1-5.1 [655 kB]
+Get: 27 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libsigsegv2 s390x 2.11-1 [29.3 kB]
+Get: 28 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x m4 s390x 1.4.18-1 [200 kB]
+Get: 29 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x autoconf all 2.69-11 [341 kB]
+Get: 30 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x autotools-dev all 20161112.1+nmu1 [74.2 kB]
+Get: 31 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x automake all 1:1.15.1-3 [736 kB]
+Get: 32 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x autopoint all 0.19.8.1-4 [434 kB]
+Get: 33 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libtool all 2.4.6-2 [545 kB]
+Get: 34 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x dh-autoreconf all 15 [16.2 kB]
+Get: 35 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libarchive-zip-perl all 1.59-1 [95.5 kB]
+Get: 36 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
+Get: 37 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libtimedate-perl all 2.3000-2 [42.2 kB]
+Get: 38 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x dh-strip-nondeterminism all 0.040-1 [11.8 kB]
+Get: 39 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libglib2.0-0 s390x 2.54.2-1 [2733 kB]
+Get: 40 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libcroco3 s390x 0.6.12-1 [138 kB]
+Get: 41 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x gettext s390x 0.19.8.1-4 [1273 kB]
+Get: 42 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get: 43 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x po-debconf all 1.0.20 [247 kB]
+Get: 44 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x debhelper all 10.10.9 [975 kB]
+Get: 45 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libbz2-dev s390x 1.0.6-8.1 [31.1 kB]
+Get: 46 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libnghttp2-14 s390x 1.28.0-1 [80.3 kB]
+Get: 47 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libpsl5 s390x 0.19.1-4 [44.1 kB]
+Get: 48 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-1+b1 [58.0 kB]
+Get: 49 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libssh2-1 s390x 1.8.0-1 [134 kB]
+Get: 50 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libcurl3-gnutls s390x 7.57.0-1 [294 kB]
+Get: 51 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libgslcblas0 s390x 2.4+dfsg-6 [81.7 kB]
+Get: 52 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libgsl23 s390x 2.4+dfsg-6 [741 kB]
+Get: 53 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libgsl-dev s390x 2.4+dfsg-6 [888 kB]
+Get: 54 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x liblzma-dev s390x 5.2.2-1.3 [295 kB]
+Get: 55 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x libio-pty-perl s390x 1:1.08-1.1+b4 [33.9 kB]
+Get: 56 http://ftp-stud.hs-esslingen.de/debian unstable/main s390x zlib1g-dev s390x 1:1.2.8.dfsg-5 [204 kB]
+Fetched 25.3 MB in 1s (18.3 MB/s)
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package groff-base.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11719 files and directories currently installed.)
+Preparing to unpack .../00-groff-base_1.22.3-9_s390x.deb ...
+Unpacking groff-base (1.22.3-9) ...
+Selecting previously unselected package libbsd0:s390x.
+Preparing to unpack .../01-libbsd0_0.8.6-3_s390x.deb ...
+Unpacking libbsd0:s390x (0.8.6-3) ...
+Selecting previously unselected package libncurses5:s390x.
+Preparing to unpack .../02-libncurses5_6.0+20171125-1_s390x.deb ...
+Unpacking libncurses5:s390x (6.0+20171125-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../03-bsdmainutils_9.0.14_s390x.deb ...
+Unpacking bsdmainutils (9.0.14) ...
+Selecting previously unselected package libpipeline1:s390x.
+Preparing to unpack .../04-libpipeline1_1.5.0-1_s390x.deb ...
+Unpacking libpipeline1:s390x (1.5.0-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../05-man-db_2.7.6.1-4_s390x.deb ...
+Unpacking man-db (2.7.6.1-4) ...
+Selecting previously unselected package libssl1.1:s390x.
+Preparing to unpack .../06-libssl1.1_1.1.0g-2_s390x.deb ...
+Unpacking libssl1.1:s390x (1.1.0g-2) ...
+Selecting previously unselected package libmagic-mgc.
+Preparing to unpack .../07-libmagic-mgc_1%3a5.32-1_s390x.deb ...
+Unpacking libmagic-mgc (1:5.32-1) ...
+Selecting previously unselected package libmagic1:s390x.
+Preparing to unpack .../08-libmagic1_1%3a5.32-1_s390x.deb ...
+Unpacking libmagic1:s390x (1:5.32-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../09-file_1%3a5.32-1_s390x.deb ...
+Unpacking file (1:5.32-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../10-gettext-base_0.19.8.1-4_s390x.deb ...
+Unpacking gettext-base (0.19.8.1-4) ...
+Selecting previously unselected package libkeyutils1:s390x.
+Preparing to unpack .../11-libkeyutils1_1.5.9-9.2_s390x.deb ...
+Unpacking libkeyutils1:s390x (1.5.9-9.2) ...
+Selecting previously unselected package libkrb5support0:s390x.
+Preparing to unpack .../12-libkrb5support0_1.15.2-2_s390x.deb ...
+Unpacking libkrb5support0:s390x (1.15.2-2) ...
+Selecting previously unselected package libk5crypto3:s390x.
+Preparing to unpack .../13-libk5crypto3_1.15.2-2_s390x.deb ...
+Unpacking libk5crypto3:s390x (1.15.2-2) ...
+Selecting previously unselected package libkrb5-3:s390x.
+Preparing to unpack .../14-libkrb5-3_1.15.2-2_s390x.deb ...
+Unpacking libkrb5-3:s390x (1.15.2-2) ...
+Selecting previously unselected package libgssapi-krb5-2:s390x.
+Preparing to unpack .../15-libgssapi-krb5-2_1.15.2-2_s390x.deb ...
+Unpacking libgssapi-krb5-2:s390x (1.15.2-2) ...
+Selecting previously unselected package libsasl2-modules-db:s390x.
+Preparing to unpack .../16-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3_s390x.deb ...
+Unpacking libsasl2-modules-db:s390x (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libsasl2-2:s390x.
+Preparing to unpack .../17-libsasl2-2_2.1.27~101-g0780600+dfsg-3_s390x.deb ...
+Unpacking libsasl2-2:s390x (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libldap-common.
+Preparing to unpack .../18-libldap-common_2.4.45+dfsg-1_all.deb ...
+Unpacking libldap-common (2.4.45+dfsg-1) ...
+Selecting previously unselected package libldap-2.4-2:s390x.
+Preparing to unpack .../19-libldap-2.4-2_2.4.45+dfsg-1_s390x.deb ...
+Unpacking libldap-2.4-2:s390x (2.4.45+dfsg-1) ...
+Selecting previously unselected package libicu57:s390x.
+Preparing to unpack .../20-libicu57_57.1-8_s390x.deb ...
+Unpacking libicu57:s390x (57.1-8) ...
+Selecting previously unselected package libxml2:s390x.
+Preparing to unpack .../21-libxml2_2.9.4+dfsg1-5.1_s390x.deb ...
+Unpacking libxml2:s390x (2.9.4+dfsg1-5.1) ...
+Selecting previously unselected package libsigsegv2:s390x.
+Preparing to unpack .../22-libsigsegv2_2.11-1_s390x.deb ...
+Unpacking libsigsegv2:s390x (2.11-1) ...
+Selecting previously unselected package m4.
+Preparing to unpack .../23-m4_1.4.18-1_s390x.deb ...
+Unpacking m4 (1.4.18-1) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../24-autoconf_2.69-11_all.deb ...
+Unpacking autoconf (2.69-11) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../25-autotools-dev_20161112.1+nmu1_all.deb ...
+Unpacking autotools-dev (20161112.1+nmu1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../26-automake_1%3a1.15.1-3_all.deb ...
+Unpacking automake (1:1.15.1-3) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../27-autopoint_0.19.8.1-4_all.deb ...
+Unpacking autopoint (0.19.8.1-4) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../28-libtool_2.4.6-2_all.deb ...
+Unpacking libtool (2.4.6-2) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../29-dh-autoreconf_15_all.deb ...
+Unpacking dh-autoreconf (15) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../30-libarchive-zip-perl_1.59-1_all.deb ...
+Unpacking libarchive-zip-perl (1.59-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../31-libfile-stripnondeterminism-perl_0.040-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.040-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../32-libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../33-dh-strip-nondeterminism_0.040-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.040-1) ...
+Selecting previously unselected package libglib2.0-0:s390x.
+Preparing to unpack .../34-libglib2.0-0_2.54.2-1_s390x.deb ...
+Unpacking libglib2.0-0:s390x (2.54.2-1) ...
+Selecting previously unselected package libcroco3:s390x.
+Preparing to unpack .../35-libcroco3_0.6.12-1_s390x.deb ...
+Unpacking libcroco3:s390x (0.6.12-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../36-gettext_0.19.8.1-4_s390x.deb ...
+Unpacking gettext (0.19.8.1-4) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../37-intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../38-po-debconf_1.0.20_all.deb ...
+Unpacking po-debconf (1.0.20) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../39-debhelper_10.10.9_all.deb ...
+Unpacking debhelper (10.10.9) ...
+Selecting previously unselected package libbz2-dev:s390x.
+Preparing to unpack .../40-libbz2-dev_1.0.6-8.1_s390x.deb ...
+Unpacking libbz2-dev:s390x (1.0.6-8.1) ...
+Selecting previously unselected package libnghttp2-14:s390x.
+Preparing to unpack .../41-libnghttp2-14_1.28.0-1_s390x.deb ...
+Unpacking libnghttp2-14:s390x (1.28.0-1) ...
+Selecting previously unselected package libpsl5:s390x.
+Preparing to unpack .../42-libpsl5_0.19.1-4_s390x.deb ...
+Unpacking libpsl5:s390x (0.19.1-4) ...
+Selecting previously unselected package librtmp1:s390x.
+Preparing to unpack .../43-librtmp1_2.4+20151223.gitfa8646d.1-1+b1_s390x.deb ...
+Unpacking librtmp1:s390x (2.4+20151223.gitfa8646d.1-1+b1) ...
+Selecting previously unselected package libssh2-1:s390x.
+Preparing to unpack .../44-libssh2-1_1.8.0-1_s390x.deb ...
+Unpacking libssh2-1:s390x (1.8.0-1) ...
+Selecting previously unselected package libcurl3-gnutls:s390x.
+Preparing to unpack .../45-libcurl3-gnutls_7.57.0-1_s390x.deb ...
+Unpacking libcurl3-gnutls:s390x (7.57.0-1) ...
+Selecting previously unselected package libgslcblas0:s390x.
+Preparing to unpack .../46-libgslcblas0_2.4+dfsg-6_s390x.deb ...
+Unpacking libgslcblas0:s390x (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl23:s390x.
+Preparing to unpack .../47-libgsl23_2.4+dfsg-6_s390x.deb ...
+Unpacking libgsl23:s390x (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl-dev.
+Preparing to unpack .../48-libgsl-dev_2.4+dfsg-6_s390x.deb ...
+Unpacking libgsl-dev (2.4+dfsg-6) ...
+Selecting previously unselected package libhts2:s390x.
+Preparing to unpack .../49-libhts2_1.5-6_s390x.deb ...
+Unpacking libhts2:s390x (1.5-6) ...
+Selecting previously unselected package liblzma-dev:s390x.
+Preparing to unpack .../50-liblzma-dev_5.2.2-1.3_s390x.deb ...
+Unpacking liblzma-dev:s390x (5.2.2-1.3) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../51-tabix_1.5-6_s390x.deb ...
+Unpacking tabix (1.5-6) ...
+Selecting previously unselected package libhts-dev:s390x.
+Preparing to unpack .../52-libhts-dev_1.5-6_s390x.deb ...
+Unpacking libhts-dev:s390x (1.5-6) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../53-libio-pty-perl_1%3a1.08-1.1+b4_s390x.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b4) ...
+Selecting previously unselected package zlib1g-dev:s390x.
+Preparing to unpack .../54-zlib1g-dev_1%3a1.2.8.dfsg-5_s390x.deb ...
+Unpacking zlib1g-dev:s390x (1:1.2.8.dfsg-5) ...
+Selecting previously unselected package sbuild-build-depends-bcftools-dummy.
+Preparing to unpack .../55-sbuild-build-depends-bcftools-dummy_0.invalid.0_s390x.deb ...
+Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Setting up libncurses5:s390x (6.0+20171125-1) ...
+Setting up libbz2-dev:s390x (1.0.6-8.1) ...
+Setting up libarchive-zip-perl (1.59-1) ...
+Setting up libnghttp2-14:s390x (1.28.0-1) ...
+Setting up libio-pty-perl (1:1.08-1.1+b4) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libsigsegv2:s390x (2.11-1) ...
+Setting up libldap-common (2.4.45+dfsg-1) ...
+Setting up libpsl5:s390x (0.19.1-4) ...
+Setting up groff-base (1.22.3-9) ...
+Setting up libglib2.0-0:s390x (2.54.2-1) ...
+No schema files found: doing nothing.
+Setting up libsasl2-modules-db:s390x (2.1.27~101-g0780600+dfsg-3) ...
+Setting up libsasl2-2:s390x (2.1.27~101-g0780600+dfsg-3) ...
+Setting up gettext-base (0.19.8.1-4) ...
+Setting up libpipeline1:s390x (1.5.0-1) ...
+Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-1+b1) ...
+Setting up m4 (1.4.18-1) ...
+Setting up libicu57:s390x (57.1-8) ...
+Setting up libbsd0:s390x (0.8.6-3) ...
+Setting up libxml2:s390x (2.9.4+dfsg1-5.1) ...
+Setting up libmagic-mgc (1:5.32-1) ...
+Setting up libmagic1:s390x (1:5.32-1) ...
+Setting up libcroco3:s390x (0.6.12-1) ...
+Setting up libssh2-1:s390x (1.8.0-1) ...
+Processing triggers for libc-bin (2.25-3) ...
+Setting up autotools-dev (20161112.1+nmu1) ...
+Setting up libldap-2.4-2:s390x (2.4.45+dfsg-1) ...
+Setting up libssl1.1:s390x (1.1.0g-2) ...
+Setting up liblzma-dev:s390x (5.2.2-1.3) ...
+Setting up libkeyutils1:s390x (1.5.9-9.2) ...
+Setting up bsdmainutils (9.0.14) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libgslcblas0:s390x (2.4+dfsg-6) ...
+Setting up autopoint (0.19.8.1-4) ...
+Setting up zlib1g-dev:s390x (1:1.2.8.dfsg-5) ...
+Setting up libfile-stripnondeterminism-perl (0.040-1) ...
+Setting up libgsl23:s390x (2.4+dfsg-6) ...
+Setting up gettext (0.19.8.1-4) ...
+Setting up libgsl-dev (2.4+dfsg-6) ...
+Setting up autoconf (2.69-11) ...
+Setting up file (1:5.32-1) ...
+Setting up libkrb5support0:s390x (1.15.2-2) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up automake (1:1.15.1-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
+Setting up man-db (2.7.6.1-4) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libtool (2.4.6-2) ...
+Setting up libk5crypto3:s390x (1.15.2-2) ...
+Setting up po-debconf (1.0.20) ...
+Setting up libkrb5-3:s390x (1.15.2-2) ...
+Setting up libgssapi-krb5-2:s390x (1.15.2-2) ...
+Setting up libcurl3-gnutls:s390x (7.57.0-1) ...
+Setting up tabix (1.5-6) ...
+Setting up libhts2:s390x (1.5-6) ...
+Setting up libhts-dev:s390x (1.5-6) ...
+Setting up dh-autoreconf (15) ...
+Setting up dh-strip-nondeterminism (0.040-1) ...
+Setting up debhelper (10.10.9) ...
+Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.25-3) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+
++------------------------------------------------------------------------------+
+| Build environment |
++------------------------------------------------------------------------------+
+
+Kernel: Linux 4.9.0-4-s390x s390x (s390x)
+Toolchain package versions: binutils_2.29.1-11 dpkg-dev_1.19.0.4 g++-7_7.2.0-17 gcc-7_7.2.0-17 libc6-dev_2.25-3 libstdc++-7-dev_7.2.0-17 libstdc++6_7.2.0-17 linux-libc-dev_4.14.2-1
+Package versions: adduser_3.116 apt_1.6~alpha5 aptitude_0.8.10-1 aptitude-common_0.8.10-1 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-11 binutils-common_2.29.1-11 binutils-s390x-linux-gnu_2.29.1-11 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 coreutils_8.28-1 cpp_4:7.2.0-1d1 cpp-7_7.2.0-17 dash_0.5.8-2.5 debconf_1.5.65 debhelper_10.10.9 debian-archive- [...]
+
++------------------------------------------------------------------------------+
+| Build |
++------------------------------------------------------------------------------+
+
+
+Unpack source
+-------------
+
+gpgv: unknown type of key resource 'trustedkeys.kbx'
+gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
+gpgv: Signature made Mon Dec 11 14:53:09 2017 UTC
+gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
+gpgv: issuer "tillea at rki.de"
+gpgv: Can't check signature: No public key
+dpkg-source: warning: failed to verify signature on ./bcftools_1.6-1.dsc
+dpkg-source: info: extracting bcftools in /<<PKGBUILDDIR>>
+dpkg-source: info: unpacking bcftools_1.6.orig.tar.gz
+dpkg-source: info: unpacking bcftools_1.6-1.debian.tar.xz
+dpkg-source: info: applying tests-pluginpath.patch
+dpkg-source: info: applying test-regidx-unsigned-char.patch
+dpkg-source: info: applying fix-test_vcf_query.patch
+
+Check disk space
+----------------
+
+Sufficient free space for build
+
+User Environment
+----------------
+
+APT_CONFIG=/var/lib/sbuild/apt.conf
+DEB_BUILD_OPTIONS=parallel=2
+HOME=/sbuild-nonexistent
+LC_ALL=POSIX
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=experimental-s390x-sbuild
+SCHROOT_CHROOT_NAME=experimental-s390x-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1009
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=experimental-s390x-sbuild-5991431c-cb8c-4fb6-9191-caea4f6f287f
+SCHROOT_UID=2952
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
+XDG_RUNTIME_DIR=/run/user/2952
+XDG_SESSION_ID=1
+
+dpkg-buildpackage
+-----------------
+
+dpkg-buildpackage: info: source package bcftools
+dpkg-buildpackage: info: source version 1.6-1
+dpkg-buildpackage: info: source distribution experimental
+ dpkg-source --before-build bcftools-1.6
+dpkg-buildpackage: info: host architecture s390x
+ fakeroot debian/rules clean
+rm -f config.mk && touch config.mk
+dh clean --parallel
+ dh_auto_clean
+ make -j2 distclean
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+rm -f test/*.o test/*~
+rm -f plugins/*.so plugins/*.P
+rm -rf plugins/*.dSYM
+rm -f gmon.out *.o *~ version.h plugins/*.so plugins/*.P
+rm -rf *.dSYM plugins/*.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 '/<<PKGBUILDDIR>>'
+ dh_clean
+ debian/rules build-arch
+dh build-arch --parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_autoreconf
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+rm -f config.mk && touch config.mk
+export MAKEFLAGS="-s"; dh_autoreconf
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+dh_auto_configure -- \
+--with-htslib=system \
+--enable-gsl \
+--with-cblas=gslcblas \
+--with-bcf-plugin-dir=/usr/lib/s390x-linux-gnu/bcftools
+ ./configure --build=s390x-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/s390x-linux-gnu --libexecdir=\${prefix}/lib/s390x-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/s390x-linux-gnu/bcftools
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... no
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking shared library type... plain .so
+checking for library containing dlopen... -ldl
+checking if the compiler accepts -rdynamic... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ dh_auto_build -a -O--parallel
+ make -j2
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+echo '#define BCFTOOLS_VERSION "1.6"' > version.h
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/s390x-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c
+gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl
+gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -ldl -ldl
+gcc -rdynamic -pthread -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 vcfplugin.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 ccall.o em.o prob1.o kmin.o -l [...]
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ dh_auto_test -a -O--parallel
+ make -j2 test VERBOSE=1
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+./test/test-rbuf
+Inserted 1-9 starting at offset 5:
+ 5 6 7 8 9 0 1 2 3
+ 1 2 3 4 5 6 7 8 9
+4th is 4
+Deleting 1-2:
+ 7 8 9 0 1 2 3
+ 3 4 5 6 7 8 9
+Prepending 0-8:
+ 8 9 0 1 2 3 4 5 6 7
+ 8 7 6 5 4 3 2 1 0 3
+Expanding:
+ 8 9 10 11 12 13 14 15 16 17
+ 8 7 6 5 4 3 2 1 0 3
+./test/test-regidx
+REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix=
+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/2tkYnqlQrG/merge.a.vcf.gz 2:3199812-3199812
+.. ok
+
+test_tabix:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/2tkYnqlQrG/merge.a.bcf 2:3199812-3199812
+.. ok
+
+test_tabix:
+ tabix /tmp/2tkYnqlQrG/merge.a.vcf.gz 1:3000151-3000151
+.. ok
+
+test_tabix:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/2tkYnqlQrG/merge.a.bcf 1:3000151-3000151
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/2tkYnqlQrG/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/2tkYnqlQrG/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/2tkYnqlQrG/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/2tkYnqlQrG/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/2tkYnqlQrG/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/2tkYnqlQrG/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/2tkYnqlQrG/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/2tkYnqlQrG/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/2tkYnqlQrG/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/2tkYnqlQrG/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/2tkYnqlQrG/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/2tkYnqlQrG/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/2tkYnqlQrG/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/2tkYnqlQrG/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/2tkYnqlQrG/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/2tkYnqlQrG/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/2tkYnqlQrG/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/2tkYnqlQrG/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/2tkYnqlQrG/empty.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/2tkYnqlQrG/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/2tkYnqlQrG/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/2tkYnqlQrG/empty.bcf
+.. ok
+
+test_vcf_check:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/2tkYnqlQrG/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check_merge:
+ /<<PKGBUILDDIR>>/misc/plot-vcfstats -m /tmp/2tkYnqlQrG/check.1.chk /tmp/2tkYnqlQrG/check.2.chk /tmp/2tkYnqlQrG/check.3.chk /tmp/2tkYnqlQrG/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/2tkYnqlQrG/stats.a.vcf.gz /tmp/2tkYnqlQrG/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s B /tmp/2tkYnqlQrG/stats.a.vcf.gz /tmp/2tkYnqlQrG/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/2tkYnqlQrG/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 /tmp/2tkYnqlQrG/isec.a.vcf.gz /tmp/2tkYnqlQrG/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 /tmp/2tkYnqlQrG/isec.a.vcf.gz /tmp/2tkYnqlQrG/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/2tkYnqlQrG/isec.a.vcf.gz /tmp/2tkYnqlQrG/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/2tkYnqlQrG/isec.a.vcf.gz /tmp/2tkYnqlQrG/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -c both /tmp/2tkYnqlQrG/isec.a.vcf.gz /tmp/2tkYnqlQrG/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -c both /tmp/2tkYnqlQrG/isec.a.vcf.gz /tmp/2tkYnqlQrG/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -c any /tmp/2tkYnqlQrG/isec.a.vcf.gz /tmp/2tkYnqlQrG/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -c any /tmp/2tkYnqlQrG/isec.a.vcf.gz /tmp/2tkYnqlQrG/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -C -c any /tmp/2tkYnqlQrG/isec.a.vcf.gz /tmp/2tkYnqlQrG/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -C -c any /tmp/2tkYnqlQrG/isec.a.vcf.gz /tmp/2tkYnqlQrG/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec2:
+ /<<PKGBUILDDIR>>/bcftools isec --no-version -T /tmp/2tkYnqlQrG/isec.tab.gz /tmp/2tkYnqlQrG/isec.a.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/isec.tab.out
+ /<<PKGBUILDDIR>>/test/isec.tab.out.new
+.. failed ...
+
+test_vcf_isec2:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -T /tmp/2tkYnqlQrG/isec.tab.gz /tmp/2tkYnqlQrG/isec.a.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/isec.tab.out
+ /<<PKGBUILDDIR>>/test/isec.tab.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples /tmp/2tkYnqlQrG/merge.a.vcf.gz /tmp/2tkYnqlQrG/merge.b.vcf.gz /tmp/2tkYnqlQrG/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.out
+ /<<PKGBUILDDIR>>/test/merge.abc.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples /tmp/2tkYnqlQrG/merge.a.vcf.gz /tmp/2tkYnqlQrG/merge.b.vcf.gz /tmp/2tkYnqlQrG/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.out
+ /<<PKGBUILDDIR>>/test/merge.abc.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -Fx /tmp/2tkYnqlQrG/merge.a.vcf.gz /tmp/2tkYnqlQrG/merge.b.vcf.gz /tmp/2tkYnqlQrG/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -Fx /tmp/2tkYnqlQrG/merge.a.vcf.gz /tmp/2tkYnqlQrG/merge.b.vcf.gz /tmp/2tkYnqlQrG/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -0 /tmp/2tkYnqlQrG/merge.a.vcf.gz /tmp/2tkYnqlQrG/merge.b.vcf.gz /tmp/2tkYnqlQrG/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -0 /tmp/2tkYnqlQrG/merge.a.vcf.gz /tmp/2tkYnqlQrG/merge.b.vcf.gz /tmp/2tkYnqlQrG/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m none /tmp/2tkYnqlQrG/merge.2.a.vcf.gz /tmp/2tkYnqlQrG/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.none.out
+ /<<PKGBUILDDIR>>/test/merge.2.none.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m none /tmp/2tkYnqlQrG/merge.2.a.vcf.gz /tmp/2tkYnqlQrG/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.none.out
+ /<<PKGBUILDDIR>>/test/merge.2.none.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m both /tmp/2tkYnqlQrG/merge.2.a.vcf.gz /tmp/2tkYnqlQrG/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.both.out
+ /<<PKGBUILDDIR>>/test/merge.2.both.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m both /tmp/2tkYnqlQrG/merge.2.a.vcf.gz /tmp/2tkYnqlQrG/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.both.out
+ /<<PKGBUILDDIR>>/test/merge.2.both.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m all /tmp/2tkYnqlQrG/merge.2.a.vcf.gz /tmp/2tkYnqlQrG/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.all.out
+ /<<PKGBUILDDIR>>/test/merge.2.all.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m all /tmp/2tkYnqlQrG/merge.2.a.vcf.gz /tmp/2tkYnqlQrG/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.all.out
+ /<<PKGBUILDDIR>>/test/merge.2.all.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/2tkYnqlQrG/merge.3.a.vcf.gz /tmp/2tkYnqlQrG/merge.3.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.3.out
+ /<<PKGBUILDDIR>>/test/merge.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/2tkYnqlQrG/merge.3.a.vcf.gz /tmp/2tkYnqlQrG/merge.3.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.3.out
+ /<<PKGBUILDDIR>>/test/merge.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m id /tmp/2tkYnqlQrG/merge.4.a.vcf.gz /tmp/2tkYnqlQrG/merge.4.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.4.out
+ /<<PKGBUILDDIR>>/test/merge.4.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m id /tmp/2tkYnqlQrG/merge.4.a.vcf.gz /tmp/2tkYnqlQrG/merge.4.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.4.out
+ /<<PKGBUILDDIR>>/test/merge.4.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - /tmp/2tkYnqlQrG/gvcf.merge.1.vcf.gz /tmp/2tkYnqlQrG/gvcf.merge.2.vcf.gz /tmp/2tkYnqlQrG/gvcf.merge.3.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - /tmp/2tkYnqlQrG/gvcf.merge.1.vcf.gz /tmp/2tkYnqlQrG/gvcf.merge.2.vcf.gz /tmp/2tkYnqlQrG/gvcf.merge.3.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - /tmp/2tkYnqlQrG/merge.gvcf.2.a.vcf.gz /tmp/2tkYnqlQrG/merge.gvcf.2.b.vcf.gz /tmp/2tkYnqlQrG/merge.gvcf.2.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - /tmp/2tkYnqlQrG/merge.gvcf.2.a.vcf.gz /tmp/2tkYnqlQrG/merge.gvcf.2.b.vcf.gz /tmp/2tkYnqlQrG/merge.gvcf.2.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - -i SRC:join /tmp/2tkYnqlQrG/merge.gvcf.3.a.vcf.gz /tmp/2tkYnqlQrG/merge.gvcf.3.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/2tkYnqlQrG/merge.gvcf.3.a.vcf.gz /tmp/2tkYnqlQrG/merge.gvcf.3.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version /tmp/2tkYnqlQrG/merge.5.a.vcf.gz /tmp/2tkYnqlQrG/merge.5.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob /tmp/2tkYnqlQrG/merge.5.a.vcf.gz /tmp/2tkYnqlQrG/merge.5.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/2tkYnqlQrG/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XRI\n' -i'XRI[*]>1111'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' /tmp/2tkYnqlQrG/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/2tkYnqlQrG/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/2tkYnqlQrG/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10' /tmp/2tkYnqlQrG/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/2tkYnqlQrG/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/2tkYnqlQrG/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/2tkYnqlQrG/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/2tkYnqlQrG/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/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/2tkYnqlQrG/view.vectors.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/query.12.out
+ /<<PKGBUILDDIR>>/test/query.12.out.new
+.. failed ...
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/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'
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/query.12.out
+ /<<PKGBUILDDIR>>/test/query.12.out.new
+.. failed ...
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' /tmp/2tkYnqlQrG/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' /tmp/2tkYnqlQrG/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' /tmp/2tkYnqlQrG/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' /tmp/2tkYnqlQrG/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/2tkYnqlQrG/query.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%LINE' /tmp/2tkYnqlQrG/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%LINE'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/2tkYnqlQrG/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/2tkYnqlQrG/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/2tkYnqlQrG/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/2tkYnqlQrG/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/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/2tkYnqlQrG/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/filter-missing-floats.vcf.gz | /<<PKGBUILDDIR>>/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:
+ /<<PKGBUILDDIR>>/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/2tkYnqlQrG/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/filter-missing-floats.vcf.gz | /<<PKGBUILDDIR>>/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:
+ /<<PKGBUILDDIR>>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/2tkYnqlQrG/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/2tkYnqlQrG/query.filter.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/query.filter.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5'
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -cx -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/2tkYnqlQrG/norm.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.out
+ /<<PKGBUILDDIR>>/test/norm.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -cx -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/2tkYnqlQrG/norm.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.out
+ /<<PKGBUILDDIR>>/test/norm.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- /tmp/2tkYnqlQrG/norm.split.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.split.out
+ /<<PKGBUILDDIR>>/test/norm.split.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- /tmp/2tkYnqlQrG/norm.split.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.split.out
+ /<<PKGBUILDDIR>>/test/norm.split.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- /tmp/2tkYnqlQrG/norm.split.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- /tmp/2tkYnqlQrG/norm.split.2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/2tkYnqlQrG/norm.split.vcf.gz 2>/dev/null
+
+ Non-zero status 255
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/2tkYnqlQrG/norm.split.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/2tkYnqlQrG/norm.merge.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.out
+ /<<PKGBUILDDIR>>/test/norm.merge.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/2tkYnqlQrG/norm.merge.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.out
+ /<<PKGBUILDDIR>>/test/norm.merge.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/2tkYnqlQrG/norm.merge.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/2tkYnqlQrG/norm.merge.2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/2tkYnqlQrG/norm.merge.3.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/2tkYnqlQrG/norm.merge.3.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.'
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ -s /tmp/2tkYnqlQrG/norm.merge.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ -s /tmp/2tkYnqlQrG/norm.merge.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -Nc s -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/2tkYnqlQrG/norm.setref.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -Nc s -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/2tkYnqlQrG/norm.setref.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/2tkYnqlQrG/norm.telomere.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/2tkYnqlQrG/norm.telomere.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/2tkYnqlQrG/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.1.out
+ /<<PKGBUILDDIR>>/test/view.1.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/2tkYnqlQrG/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.1.out
+ /<<PKGBUILDDIR>>/test/view.1.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/2tkYnqlQrG/view.vcf.gz -r20,Y
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.2.out
+ /<<PKGBUILDDIR>>/test/view.2.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/2tkYnqlQrG/view.vcf.gz -r20,Y | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.2.out
+ /<<PKGBUILDDIR>>/test/view.2.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -xs NA00003 /tmp/2tkYnqlQrG/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.3.out
+ /<<PKGBUILDDIR>>/test/view.3.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -xs NA00003 /tmp/2tkYnqlQrG/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.3.out
+ /<<PKGBUILDDIR>>/test/view.3.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/2tkYnqlQrG/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.4.out
+ /<<PKGBUILDDIR>>/test/view.4.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/2tkYnqlQrG/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.4.out
+ /<<PKGBUILDDIR>>/test/view.4.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -p /tmp/2tkYnqlQrG/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.5.out
+ /<<PKGBUILDDIR>>/test/view.5.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -p /tmp/2tkYnqlQrG/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.5.out
+ /<<PKGBUILDDIR>>/test/view.5.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -P /tmp/2tkYnqlQrG/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.6.out
+ /<<PKGBUILDDIR>>/test/view.6.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -P /tmp/2tkYnqlQrG/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.6.out
+ /<<PKGBUILDDIR>>/test/view.6.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/2tkYnqlQrG/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/2tkYnqlQrG/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -Hu /tmp/2tkYnqlQrG/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -GVsnps /tmp/2tkYnqlQrG/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.9.out
+ /<<PKGBUILDDIR>>/test/view.9.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -GVsnps /tmp/2tkYnqlQrG/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.9.out
+ /<<PKGBUILDDIR>>/test/view.9.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/2tkYnqlQrG/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.10.out
+ /<<PKGBUILDDIR>>/test/view.10.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/2tkYnqlQrG/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.10.out
+ /<<PKGBUILDDIR>>/test/view.10.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -s ^NA00003 /tmp/2tkYnqlQrG/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.exclude.out
+ /<<PKGBUILDDIR>>/test/view.exclude.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -s ^NA00003 /tmp/2tkYnqlQrG/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.exclude.out
+ /<<PKGBUILDDIR>>/test/view.exclude.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version /tmp/2tkYnqlQrG/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/view.omitgenotypes.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -G /tmp/2tkYnqlQrG/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -G /tmp/2tkYnqlQrG/view.omitgenotypes.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -HG /tmp/2tkYnqlQrG/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -a /tmp/2tkYnqlQrG/many.alleles.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -a /tmp/2tkYnqlQrG/many.alleles.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asA /tmp/2tkYnqlQrG/view.vectors.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asA /tmp/2tkYnqlQrG/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asB /tmp/2tkYnqlQrG/view.vectors.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asB /tmp/2tkYnqlQrG/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asA /tmp/2tkYnqlQrG/view.vectors.2.vcf.gz
+[E::bcf_remove_allele_set] Unexpected number of values in INFO/IAF at 1:10; expected Number=A=2, but found 1
+Error: Could not trim alleles at 1:10
+
+ Non-zero status 255
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asA /tmp/2tkYnqlQrG/view.vectors.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_remove_allele_set] Unexpected number of values in INFO/IAF at 1:10; expected Number=A=2, but found 1
+Error: Could not trim alleles at 1:10
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[0]="AAAAAA"' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[2]="C"' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[4]="EE"' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FRS[1]="BB"' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'TXT0="text"' /tmp/2tkYnqlQrG/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -T /<<PKGBUILDDIR>>/test/view.chrs.tab /tmp/2tkYnqlQrG/view.chrs.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -T /<<PKGBUILDDIR>>/test/view.chrs.tab /tmp/2tkYnqlQrG/view.chrs.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -i 'POS>=3062917' /tmp/2tkYnqlQrG/filter.2.vcf.gz 1:3062917-3157410
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -i 'POS>=3062917' /tmp/2tkYnqlQrG/filter.2.vcf.gz 1:3062917-3157410 | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'TXT0="text"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'TXT0="text"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FRS[1]="BB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FRS[1]="BB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[0]="AAAAAA"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[0]="AAAAAA"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[1]="BBB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[1]="BBB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[4]="EE"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[4]="EE"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/STR="XX"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/STR="XX"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -C5:nonmajor /tmp/2tkYnqlQrG/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -c6:nonmajor /tmp/2tkYnqlQrG/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -q0.3:major /tmp/2tkYnqlQrG/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/2tkYnqlQrG/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/2tkYnqlQrG/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/2tkYnqlQrG/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mg0 /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup.2.out
+ /<<PKGBUILDDIR>>/test/mpileup.2.out.new
+.. failed ...
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mg0 /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup.2.out
+ /<<PKGBUILDDIR>>/test/mpileup.2.out.new
+.. failed ...
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call_cAls:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mA -C alleles -T /tmp/2tkYnqlQrG/mpileup.tab.gz /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call_cAls:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mA -C alleles -T /tmp/2tkYnqlQrG/mpileup.tab.gz /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv /<<PKGBUILDDIR>>/test/mpileup.c.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv /<<PKGBUILDDIR>>/test/mpileup.c.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -mx -g2 -G2 /<<PKGBUILDDIR>>/test/filter.1.vcf | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/filter.1.out
+ /<<PKGBUILDDIR>>/test/filter.1.out.new
+.. failed ...
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -mx -g2 -G2 /<<PKGBUILDDIR>>/test/filter.1.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/filter.1.out
+ /<<PKGBUILDDIR>>/test/filter.1.out.new
+.. failed ...
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<<PKGBUILDDIR>>/test/filter.2.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'ALT="."' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'ALT="."' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S . -i 'FORMAT/TEST3<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S . -i 'FORMAT/TEST4<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="A"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="A"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="RR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="RR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="RA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="RA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="AR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="AR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="AA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="AA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="aA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="aA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="Aa"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="Aa"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HOM"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HOM"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HET"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HET"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HAP"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HAP"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -m 0 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.UQ43Fg
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -Ob -m 0 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.fz16Mg
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -m 1000 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.mmyvNb
+Merging 4 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -Ob -m 1000 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.TBeL4b
+Merging 4 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<<PKGBUILDDIR>>/test/regions.tab /tmp/2tkYnqlQrG/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<<PKGBUILDDIR>>/test/regions.tab
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /<<PKGBUILDDIR>>/test/regions.tab /tmp/2tkYnqlQrG/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/2tkYnqlQrG/regions.tab.gz /tmp/2tkYnqlQrG/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/2tkYnqlQrG/regions.tab.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/2tkYnqlQrG/regions.tab.gz /tmp/2tkYnqlQrG/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/2tkYnqlQrG/regions.bed /tmp/2tkYnqlQrG/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/2tkYnqlQrG/regions.bed
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/2tkYnqlQrG/regions.bed /tmp/2tkYnqlQrG/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/2tkYnqlQrG/regions.bed.gz /tmp/2tkYnqlQrG/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/2tkYnqlQrG/regions.bed.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/2tkYnqlQrG/regions.bed.gz /tmp/2tkYnqlQrG/regions.vcf.gz
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/2tkYnqlQrG/annotate.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/2tkYnqlQrG/annotate.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/2tkYnqlQrG/annotate2.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/2tkYnqlQrG/annotate2.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/2tkYnqlQrG/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/2tkYnqlQrG/annotate.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/2tkYnqlQrG/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/2tkYnqlQrG/annotate.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/2tkYnqlQrG/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/2tkYnqlQrG/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/2tkYnqlQrG/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/2tkYnqlQrG/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/2tkYnqlQrG/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/2tkYnqlQrG/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/2tkYnqlQrG/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/2tkYnqlQrG/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -x FORMAT /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -x FORMAT /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/2tkYnqlQrG/annots4.vcf.gz -c +INFO /tmp/2tkYnqlQrG/annotate4.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/2tkYnqlQrG/annots4.vcf.gz -c +INFO /tmp/2tkYnqlQrG/annotate4.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/2tkYnqlQrG/annots4.tab.gz -h /<<PKGBUILDDIR>>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<<PKGBUILDDIR>>/test/annotate4.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/2tkYnqlQrG/annots4.tab.gz -h /<<PKGBUILDDIR>>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<<PKGBUILDDIR>>/test/annotate4.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/2tkYnqlQrG/annots10.tab.gz -h /<<PKGBUILDDIR>>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<<PKGBUILDDIR>>/test/annotate10.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/2tkYnqlQrG/annots10.tab.gz -h /<<PKGBUILDDIR>>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<<PKGBUILDDIR>>/test/annotate10.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/2tkYnqlQrG/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/2tkYnqlQrG/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/2tkYnqlQrG/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/2tkYnqlQrG/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/2tkYnqlQrG/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<<PKGBUILDDIR>>/test/annotate2.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/2tkYnqlQrG/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<<PKGBUILDDIR>>/test/annotate2.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/2tkYnqlQrG/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/2tkYnqlQrG/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/2tkYnqlQrG/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/2tkYnqlQrG/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/2tkYnqlQrG/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/2tkYnqlQrG/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/2tkYnqlQrG/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/2tkYnqlQrG/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +missing2ref --no-version /tmp/2tkYnqlQrG/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +missing2ref --no-version /tmp/2tkYnqlQrG/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/2tkYnqlQrG/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/2tkYnqlQrG/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/2tkYnqlQrG/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/2tkYnqlQrG/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/2tkYnqlQrG/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<<PKGBUILDDIR>>/test/annotate9.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/2tkYnqlQrG/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<<PKGBUILDDIR>>/test/annotate9.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-AN-AC --no-version /tmp/2tkYnqlQrG/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-AN-AC --no-version /tmp/2tkYnqlQrG/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +dosage /tmp/2tkYnqlQrG/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +dosage /tmp/2tkYnqlQrG/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixploidy --no-version /tmp/2tkYnqlQrG/fixploidy.vcf.gz -- -s /<<PKGBUILDDIR>>/test/fixploidy.samples -p /<<PKGBUILDDIR>>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixploidy --no-version /tmp/2tkYnqlQrG/fixploidy.bcf -- -s /<<PKGBUILDDIR>>/test/fixploidy.samples -p /<<PKGBUILDDIR>>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/2tkYnqlQrG/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/2tkYnqlQrG/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/2tkYnqlQrG/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/2tkYnqlQrG/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/2tkYnqlQrG/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/2tkYnqlQrG/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/2tkYnqlQrG/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/2tkYnqlQrG/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/2tkYnqlQrG/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/2tkYnqlQrG/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/2tkYnqlQrG/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/2tkYnqlQrG/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/2tkYnqlQrG/view.vcf.gz -- -t AC -S /<<PKGBUILDDIR>>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/2tkYnqlQrG/view.bcf -- -t AC -S /<<PKGBUILDDIR>>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/2tkYnqlQrG/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/2tkYnqlQrG/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/2tkYnqlQrG/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/2tkYnqlQrG/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/2tkYnqlQrG/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +trio-switch-rate /tmp/2tkYnqlQrG/trio.vcf.gz -- -p /<<PKGBUILDDIR>>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +trio-switch-rate /tmp/2tkYnqlQrG/trio.bcf -- -p /<<PKGBUILDDIR>>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +ad-bias /tmp/2tkYnqlQrG/ad-bias.vcf.gz -- -s /<<PKGBUILDDIR>>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +ad-bias /tmp/2tkYnqlQrG/ad-bias.bcf -- -s /<<PKGBUILDDIR>>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +af-dist /tmp/2tkYnqlQrG/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +af-dist /tmp/2tkYnqlQrG/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixref /tmp/2tkYnqlQrG/fixref.2a.vcf.gz -- -f /<<PKGBUILDDIR>>/test/norm.fa -i /tmp/2tkYnqlQrG/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixref /tmp/2tkYnqlQrG/fixref.2a.bcf -- -f /<<PKGBUILDDIR>>/test/norm.fa -i /tmp/2tkYnqlQrG/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/2tkYnqlQrG/aa.vcf.gz -- -f /<<PKGBUILDDIR>>/test/aa.fa -c AA -h /<<PKGBUILDDIR>>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/aa.out
+ /<<PKGBUILDDIR>>/test/aa.out.new
+.. failed ...
+
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/2tkYnqlQrG/aa.bcf -- -f /<<PKGBUILDDIR>>/test/aa.fa -c AA -h /<<PKGBUILDDIR>>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/aa.out
+ /<<PKGBUILDDIR>>/test/aa.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/2tkYnqlQrG/ref.vcf.gz -- -f /<<PKGBUILDDIR>>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+
+ Non-zero status 1
+.. failed ...
+
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/2tkYnqlQrG/ref.bcf -- -f /<<PKGBUILDDIR>>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/ref.out
+ /<<PKGBUILDDIR>>/test/ref.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/2tkYnqlQrG/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/2tkYnqlQrG/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/2tkYnqlQrG/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/2tkYnqlQrG/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/2tkYnqlQrG/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/2tkYnqlQrG/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/2tkYnqlQrG/mendelian.vcf.gz -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/2tkYnqlQrG/mendelian.bcf -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/2tkYnqlQrG/mendelian.vcf.gz -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/2tkYnqlQrG/mendelian.bcf -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/2tkYnqlQrG/mendelian.vcf.gz -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/2tkYnqlQrG/mendelian.bcf -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version /tmp/2tkYnqlQrG/concat.1.a.vcf.gz /tmp/2tkYnqlQrG/concat.1.b.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob /tmp/2tkYnqlQrG/concat.1.a.vcf.gz /tmp/2tkYnqlQrG/concat.1.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.1.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.1.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version /tmp/2tkYnqlQrG/concat.1.a.bcf /tmp/2tkYnqlQrG/concat.1.b.bcf
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob /tmp/2tkYnqlQrG/concat.1.a.bcf /tmp/2tkYnqlQrG/concat.1.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -a /tmp/2tkYnqlQrG/concat.2.a.vcf.gz /tmp/2tkYnqlQrG/concat.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -a /tmp/2tkYnqlQrG/concat.2.a.vcf.gz /tmp/2tkYnqlQrG/concat.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -a /tmp/2tkYnqlQrG/concat.2.a.bcf /tmp/2tkYnqlQrG/concat.2.b.bcf
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -a /tmp/2tkYnqlQrG/concat.2.a.bcf /tmp/2tkYnqlQrG/concat.2.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -aD /tmp/2tkYnqlQrG/concat.2.a.vcf.gz /tmp/2tkYnqlQrG/concat.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -aD /tmp/2tkYnqlQrG/concat.2.a.vcf.gz /tmp/2tkYnqlQrG/concat.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -aD /tmp/2tkYnqlQrG/concat.2.a.bcf /tmp/2tkYnqlQrG/concat.2.b.bcf
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -aD /tmp/2tkYnqlQrG/concat.2.a.bcf /tmp/2tkYnqlQrG/concat.2.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -l /tmp/2tkYnqlQrG/concat.3.a.vcf.gz /tmp/2tkYnqlQrG/concat.3.b.vcf.gz /tmp/2tkYnqlQrG/concat.3.0.vcf.gz /tmp/2tkYnqlQrG/concat.3.c.vcf.gz /tmp/2tkYnqlQrG/concat.3.d.vcf.gz /tmp/2tkYnqlQrG/concat.3.e.vcf.gz /tmp/2tkYnqlQrG/concat.3.f.vcf.gz
+[E::vcf_format] Invalid BCF, the FORMAT tag id=-13056 not present in the header
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -l /tmp/2tkYnqlQrG/concat.3.a.vcf.gz /tmp/2tkYnqlQrG/concat.3.b.vcf.gz /tmp/2tkYnqlQrG/concat.3.0.vcf.gz /tmp/2tkYnqlQrG/concat.3.c.vcf.gz /tmp/2tkYnqlQrG/concat.3.d.vcf.gz /tmp/2tkYnqlQrG/concat.3.e.vcf.gz /tmp/2tkYnqlQrG/concat.3.f.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+GT is not present at 2:280. (This warning is printed only once.)
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -13056
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out.new
+.. failed ...
+
+[W::bcf_record_check] Bad BCF record: Invalid INFO id -14336
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -l /tmp/2tkYnqlQrG/concat.3.a.bcf /tmp/2tkYnqlQrG/concat.3.b.bcf /tmp/2tkYnqlQrG/concat.3.0.bcf /tmp/2tkYnqlQrG/concat.3.c.bcf /tmp/2tkYnqlQrG/concat.3.d.bcf /tmp/2tkYnqlQrG/concat.3.e.bcf /tmp/2tkYnqlQrG/concat.3.f.bcf
+[W::bcf_record_check] Bad BCF record: Invalid INFO id -14336
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080
+[E::vcf_format] Invalid BCF, the FORMAT tag id=-13056 not present in the header
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -l /tmp/2tkYnqlQrG/concat.3.a.bcf /tmp/2tkYnqlQrG/concat.3.b.bcf /tmp/2tkYnqlQrG/concat.3.0.bcf /tmp/2tkYnqlQrG/concat.3.c.bcf /tmp/2tkYnqlQrG/concat.3.d.bcf /tmp/2tkYnqlQrG/concat.3.e.bcf /tmp/2tkYnqlQrG/concat.3.f.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[W::bcf_record_check] Bad BCF record: Invalid INFO id -14336
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -13056
+Random seed for test_naive_concat: 2934497501
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out.new
+.. failed ...
+
+test_naive_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --naive /tmp/2tkYnqlQrG/naive_concat.0.bcf /tmp/2tkYnqlQrG/naive_concat.1.bcf /tmp/2tkYnqlQrG/naive_concat.2.bcf /tmp/2tkYnqlQrG/naive_concat.3.bcf /tmp/2tkYnqlQrG/naive_concat.4.bcf /tmp/2tkYnqlQrG/naive_concat.5.bcf /tmp/2tkYnqlQrG/naive_concat.6.bcf /tmp/2tkYnqlQrG/naive_concat.7.bcf /tmp/2tkYnqlQrG/naive_concat.8.bcf /tmp/2tkYnqlQrG/naive_concat.9.bcf | /<<PKGBUILDDIR>>/bcftools view -H
+[E::hts_realloc_or_die] Cannot allocate memory
+Failed to open -: unknown file type
+
+ Non-zero status 255
+.. failed ...
+
+test_naive_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --naive /tmp/2tkYnqlQrG/naive_concat.0.vcf.gz /tmp/2tkYnqlQrG/naive_concat.1.vcf.gz /tmp/2tkYnqlQrG/naive_concat.2.vcf.gz /tmp/2tkYnqlQrG/naive_concat.3.vcf.gz /tmp/2tkYnqlQrG/naive_concat.4.vcf.gz /tmp/2tkYnqlQrG/naive_concat.5.vcf.gz /tmp/2tkYnqlQrG/naive_concat.6.vcf.gz /tmp/2tkYnqlQrG/naive_concat.7.vcf.gz /tmp/2tkYnqlQrG/naive_concat.8.vcf.gz /tmp/2tkYnqlQrG/naive_concat.9.vcf.gz | /<<PKGBUILDDIR>>/bcftools view -H
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.naive.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.naive.vcf.out.new
+.. failed ...
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /tmp/2tkYnqlQrG/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/2tkYnqlQrG/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /tmp/2tkYnqlQrG/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/2tkYnqlQrG/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /tmp/2tkYnqlQrG/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/2tkYnqlQrG/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /tmp/2tkYnqlQrG/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/2tkYnqlQrG/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /tmp/2tkYnqlQrG/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/2tkYnqlQrG/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /tmp/2tkYnqlQrG/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/2tkYnqlQrG/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /tmp/2tkYnqlQrG/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/2tkYnqlQrG/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /tmp/2tkYnqlQrG/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/2tkYnqlQrG/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /tmp/2tkYnqlQrG/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/2tkYnqlQrG/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /tmp/2tkYnqlQrG/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/2tkYnqlQrG/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /<<PKGBUILDDIR>>/test/empty.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/empty.vcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /tmp/2tkYnqlQrG/empty.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/2tkYnqlQrG/empty.bcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /tmp/2tkYnqlQrG/empty.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/2tkYnqlQrG/empty.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/2tkYnqlQrG/rename.map -Ov /tmp/2tkYnqlQrG/annotate.bcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/2tkYnqlQrG/rename.map -Ob /tmp/2tkYnqlQrG/annotate.bcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/2tkYnqlQrG/rename.map -Ov /<<PKGBUILDDIR>>/test/annotate.vcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/2tkYnqlQrG/rename.map -Ob /<<PKGBUILDDIR>>/test/annotate.vcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. /tmp/2tkYnqlQrG/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- /tmp/2tkYnqlQrG/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --tag PL /tmp/2tkYnqlQrG/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --tag PL /tmp/2tkYnqlQrG/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --vcf-ids /tmp/2tkYnqlQrG/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --vcf-ids /tmp/2tkYnqlQrG/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom /tmp/2tkYnqlQrG/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom /tmp/2tkYnqlQrG/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom --vcf-ids /tmp/2tkYnqlQrG/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom --vcf-ids /tmp/2tkYnqlQrG/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h -,.,. /tmp/2tkYnqlQrG/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h -,.,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h .,-,. /tmp/2tkYnqlQrG/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h .,-,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h .,.,- /tmp/2tkYnqlQrG/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h .,.,- 2>/dev/null
+.. ok
+
+test_vcf_convert_hls2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -H /<<PKGBUILDDIR>>/test/convert.hls.gt.hap,/<<PKGBUILDDIR>>/test/convert.hls.gt.legend,/<<PKGBUILDDIR>>/test/convert.hls.gt.samples 2>/dev/null | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert_hls2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -H /<<PKGBUILDDIR>>/test/convert.hls.gt.hap,/<<PKGBUILDDIR>>/test/convert.hls.gt.legend,/<<PKGBUILDDIR>>/test/convert.hls.gt.samples -Ou 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert_hs2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample2vcf /<<PKGBUILDDIR>>/test/convert.hs.gt.hap,/<<PKGBUILDDIR>>/test/convert.hs.gt.samples 2>/dev/null | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert_hs2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample2vcf /<<PKGBUILDDIR>>/test/convert.hs.gt.hap,/<<PKGBUILDDIR>>/test/convert.hs.gt.samples -Ou 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample -,. /tmp/2tkYnqlQrG/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --hapsample -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample .,- /tmp/2tkYnqlQrG/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --hapsample .,- 2>/dev/null
+.. ok
+
+test_vcf_convert_gvcf:
+ /<<PKGBUILDDIR>>/bcftools convert --no-version --gvcf2vcf -f /<<PKGBUILDDIR>>/test/gvcf.fa /tmp/2tkYnqlQrG/convert.gvcf.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out.new
+.. failed ...
+
+test_vcf_convert_gvcf:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/2tkYnqlQrG/convert.gvcf.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --gvcf2vcf -f /<<PKGBUILDDIR>>/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out.new
+.. failed ...
+
+test_vcf_convert_tsv2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /<<PKGBUILDDIR>>/test/23andme.fa --tsv2vcf /<<PKGBUILDDIR>>/test/convert.23andme 2>/dev/null
+.. ok
+
+test_vcf_convert_tsv2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /<<PKGBUILDDIR>>/test/23andme.fa --tsv2vcf /<<PKGBUILDDIR>>/test/convert.23andme 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/2tkYnqlQrG/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/2tkYnqlQrG/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/2tkYnqlQrG/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/2tkYnqlQrG/consensus.1.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/2tkYnqlQrG/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/2tkYnqlQrG/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/2tkYnqlQrG/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/2tkYnqlQrG/consensus.2.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/2tkYnqlQrG/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -I -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/2tkYnqlQrG/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -I -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/2tkYnqlQrG/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/2tkYnqlQrG/consensus.3.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/2tkYnqlQrG/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/2tkYnqlQrG/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -c /tmp/2tkYnqlQrG/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/2tkYnqlQrG/consensus.4.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/2tkYnqlQrG/consensus2.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus2.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/2tkYnqlQrG/consensus2.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus2.fa -H 2 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/2tkYnqlQrG/empty.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa 2>/dev/null
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -b /tmp/2tkYnqlQrG/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/2tkYnqlQrG/mpileup.bam.urllist 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -b /tmp/2tkYnqlQrG/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/2tkYnqlQrG/mpileup.cram.urllist 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_csq:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq.fa -g /<<PKGBUILDDIR>>/test/csq.gff3 /<<PKGBUILDDIR>>/test/csq.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq.gff3 ...
+Indexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq.1.out
+ /<<PKGBUILDDIR>>/test/csq.1.out.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ambiguous.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+/bin/bash: line 1: 37003 Done /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ambiguous.vcf
+ 37004 | /<<PKGBUILDDIR>>/test/csq/sort-csq
+ 37005 Segmentation fault | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+
+ Non-zero status 139
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.gff /<<PKGBUILDDIR>>/test/csq/ENST00000593942/last-codon-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.gff ...
+Indexed 1 transcripts, 7 exons, 4 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.gff /<<PKGBUILDDIR>>/test/csq/ENST00000557788/long-overlap-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.gff /<<PKGBUILDDIR>>/test/csq/ENST00000545279/splice-region-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.gff ...
+Indexed 1 transcripts, 9 exons, 7 CDSs, 4 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff /<<PKGBUILDDIR>>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff /<<PKGBUILDDIR>>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff /<<PKGBUILDDIR>>/test/csq/ENST00000542803/splice-region.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff /<<PKGBUILDDIR>>/test/csq/ENST00000542803/splice-region.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff /<<PKGBUILDDIR>>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff /<<PKGBUILDDIR>>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.gff /<<PKGBUILDDIR>>/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.gff ...
+Indexed 1 transcripts, 7 exons, 6 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520868/long-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520795/long-inside-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520795/long-inside-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.gff /<<PKGBUILDDIR>>/test/csq/ENST00000519442/synon-splice-region-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff /<<PKGBUILDDIR>>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff /<<PKGBUILDDIR>>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.gff /<<PKGBUILDDIR>>/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.gff ...
+Indexed 1 transcripts, 26 exons, 26 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.gff /<<PKGBUILDDIR>>/test/csq/ENST00000436063/insert-before-utr.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.gff ...
+Indexed 1 transcripts, 7 exons, 7 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/snps.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/snps.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/insert3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/insert3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.gff /<<PKGBUILDDIR>>/test/csq/ENST00000420670/start-stop-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.gff ...
+Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.gff /<<PKGBUILDDIR>>/test/csq/ENST00000413103/long-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.gff ...
+Indexed 1 transcripts, 2 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.gff /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 2 UTRs
+Calling...
+[E::vcf_format] Invalid BCF, the INFO index is too large
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.gff /<<PKGBUILDDIR>>/test/csq/ENST00000409523/long-overlapping-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.gff /<<PKGBUILDDIR>>/test/csq/ENST00000390520/deletion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.gff /<<PKGBUILDDIR>>/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.gff /<<PKGBUILDDIR>>/test/csq/ENST00000381157/haploid-diploid.vcf | /<<PKGBUILDDIR>>/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 0 UTRs
+Calling...
+Warning: Skipping site with non-diploid/non-haploid genotypes at X:31180 C>T
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000381157/haploid-diploid.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000381157/haploid-diploid.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff /<<PKGBUILDDIR>>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff /<<PKGBUILDDIR>>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.gff /<<PKGBUILDDIR>>/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff /<<PKGBUILDDIR>>/test/csq/ENST00000373833/boundary-insertion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff /<<PKGBUILDDIR>>/test/csq/ENST00000373833/boundary-insertion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.gff /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.gff /<<PKGBUILDDIR>>/test/csq/ENST00000357367/stop-retained.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.gff ...
+Indexed 1 transcripts, 4 exons, 3 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff /<<PKGBUILDDIR>>/test/csq/ENST00000329454/boundary-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff /<<PKGBUILDDIR>>/test/csq/ENST00000329454/boundary-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff /<<PKGBUILDDIR>>/test/csq/ENST00000318249/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff /<<PKGBUILDDIR>>/test/csq/ENST00000318249/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff /<<PKGBUILDDIR>>/test/csq/ENST00000303039/not-a-stop.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff /<<PKGBUILDDIR>>/test/csq/ENST00000303039/not-a-stop.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.gff /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.gff ...
+Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs
+Calling...
+[E::vcf_format] Invalid BCF, the INFO index is too large
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff /<<PKGBUILDDIR>>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff /<<PKGBUILDDIR>>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff /<<PKGBUILDDIR>>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff /<<PKGBUILDDIR>>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.gff /<<PKGBUILDDIR>>/test/csq/ENST00000256452/intron.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.gff ...
+Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.gff /<<PKGBUILDDIR>>/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff /<<PKGBUILDDIR>>/test/csq/ENST00000218032/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff /<<PKGBUILDDIR>>/test/csq/ENST00000218032/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.fa -g /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.gff /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/synon.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.gff ...
+Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs
+Calling...
+.. ok
+
+
+Number of tests:
+ total .. 728
+ passed .. 607
+ failed .. 121
+
+Makefile:246: recipe for target 'test-plugins' failed
+make[1]: *** [test-plugins] Error 1
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+dh_auto_test: make -j2 test VERBOSE=1 returned exit code 2
+debian/rules:7: recipe for target 'build-arch' failed
+make: *** [build-arch] Error 2
+dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
+--------------------------------------------------------------------------------
+Build finished at 2017-12-11T16:08:16Z
+
+Finished
+--------
+
+
++------------------------------------------------------------------------------+
+| Cleanup |
++------------------------------------------------------------------------------+
+
+Purging /<<BUILDDIR>>
+Not cleaning session: cloned chroot in use
+E: Build failure (dpkg-buildpackage died)
+
++------------------------------------------------------------------------------+
+| Summary |
++------------------------------------------------------------------------------+
+
+Build Architecture: s390x
+Build Type: any
+Build-Space: 28984
+Build-Time: 124
+Distribution: experimental
+Fail-Stage: build
+Host Architecture: s390x
+Install-Time: 34
+Job: bcftools_1.6-1
+Machine Architecture: s390x
+Package: bcftools
+Package-Time: 182
+Source-Version: 1.6-1
+Space: 28984
+Status: attempted
+Version: 1.6-1
+--------------------------------------------------------------------------------
+Finished at 2017-12-11T16:08:16Z
+Build needed 00:03:02, 28984k disk space
diff --git a/bcftools_1.6-1_sparc64.log b/bcftools_1.6-1_sparc64.log
new file mode 100644
index 0000000..42f43bd04
--- /dev/null
+++ b/bcftools_1.6-1_sparc64.log
@@ -0,0 +1,4500 @@
+
+sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on landau.east.ru
+
++==============================================================================+
+| bcftools 1.6-1 (sparc64) Mon, 11 Dec 2017 16:46:18 +0000 |
++==============================================================================+
+
+Package: bcftools
+Version: 1.6-1
+Source Version: 1.6-1
+Distribution: experimental
+Machine Architecture: sparc64
+Host Architecture: sparc64
+Build Architecture: sparc64
+Build Type: any
+
+I: NOTICE: Log filtering will replace 'var/run/schroot/mount/experimental-sparc64-sbuild-uXKTic-163911' with '<<CHROOT>>'
+
++------------------------------------------------------------------------------+
+| Update chroot |
++------------------------------------------------------------------------------+
+
+Get:1 http://ftp.debian.org/debian unstable InRelease [240 kB]
+Get:2 http://ftp.ports.debian.org/debian-ports unstable InRelease [37.1 kB]
+Get:3 http://incoming.ports.debian.org/buildd unstable InRelease [40.0 kB]
+Get:4 http://ftp.ports.debian.org/debian-ports experimental InRelease [37.6 kB]
+Get:5 http://incoming.ports.debian.org/buildd experimental InRelease [40.0 kB]
+Get:6 http://ftp.debian.org/debian experimental InRelease [107 kB]
+Get:7 http://ftp.ports.debian.org/debian-ports unreleased InRelease [40.8 kB]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:9 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 Packages [19.5 MB]
+Get:10 http://incoming.debian.org/debian-buildd buildd-experimental InRelease [58.9 kB]
+Get:11 http://incoming.ports.debian.org/buildd unstable/main sparc64 Packages [67.6 kB]
+Get:12 http://ftp.debian.org/debian unstable/main Sources [7953 kB]
+Get:13 http://ftp.ports.debian.org/debian-ports unstable/main all Packages [8263 kB]
+Get:14 http://incoming.ports.debian.org/buildd experimental/main sparc64 Packages [18.1 kB]
+Get:15 http://ftp.debian.org/debian experimental/main Sources [262 kB]
+Get:16 http://ftp.ports.debian.org/debian-ports experimental/main sparc64 Packages [790 kB]
+Get:17 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [123 kB]
+Get:18 http://ftp.ports.debian.org/debian-ports experimental/main all Packages [396 kB]
+Get:19 http://ftp.ports.debian.org/debian-ports unreleased/main sparc64 Packages [12.1 kB]
+Get:20 http://incoming.debian.org/debian-buildd buildd-experimental/main Sources [30.7 kB]
+Fetched 38.0 MB in 15s (2469 kB/s)
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Fetch source files |
++------------------------------------------------------------------------------+
+
+
+Check APT
+---------
+
+Checking available source versions...
+
+Download source files with APT
+------------------------------
+
+Reading package lists...
+NOTICE: 'bcftools' packaging is maintained in the 'Git' version control system at:
+https://anonscm.debian.org/git/debian-med/bcftools.git
+Please use:
+git clone https://anonscm.debian.org/git/debian-med/bcftools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 2342 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (dsc) [2110 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (tar) [2333 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-experimental/main bcftools 1.6-1 (diff) [6088 B]
+Fetched 2342 kB in 2s (1105 kB/s)
+Download complete and in download only mode
+I: NOTICE: Log filtering will replace 'build/bcftools-HsJdVN/bcftools-1.6' with '<<PKGBUILDDIR>>'
+I: NOTICE: Log filtering will replace 'build/bcftools-HsJdVN' with '<<BUILDDIR>>'
+
++------------------------------------------------------------------------------+
+| 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 '/<<BUILDDIR>>/resolver-8T0hWb/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:/<<BUILDDIR>>/resolver-8T0hWb/apt_archive ./ InRelease
+Get:2 copy:/<<BUILDDIR>>/resolver-8T0hWb/apt_archive ./ Release [957 B]
+Ign:3 copy:/<<BUILDDIR>>/resolver-8T0hWb/apt_archive ./ Release.gpg
+Get:4 copy:/<<BUILDDIR>>/resolver-8T0hWb/apt_archive ./ Sources [349 B]
+Get:5 copy:/<<BUILDDIR>>/resolver-8T0hWb/apt_archive ./ Packages [434 B]
+Fetched 1740 B in 0s (70.8 kB/s)
+Reading package lists...
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Install core build dependencies (aptitude-based resolver) |
++------------------------------------------------------------------------------+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following additional packages will be installed:
+ aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+Suggested packages:
+ aptitude-doc-en | aptitude-doc apt-xapian-index debtags tasksel
+ libcwidget-dev xapian-tools
+Recommended packages:
+ libparse-debianchangelog-perl
+The following NEW packages will be installed:
+ aptitude aptitude-common libboost-filesystem1.62.0 libboost-iostreams1.62.0
+ libboost-system1.62.0 libcwidget3v5 libsigc++-2.0-0v5 libsqlite3-0
+ libxapian30
+0 upgraded, 9 newly installed, 0 to remove and 2 not upgraded.
+Need to get 4688 kB of archives.
+After this operation, 19.5 MB of additional disk space will be used.
+Get:1 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libxapian30 sparc64 1.4.5-1 [942 kB]
+Get:2 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libsqlite3-0 sparc64 3.21.0-1 [506 kB]
+Get:3 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 aptitude-common all 0.8.10-1 [1591 kB]
+Get:4 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libboost-system1.62.0 sparc64 1.62.0+dfsg-4+b3 [32.5 kB]
+Get:5 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libboost-filesystem1.62.0 sparc64 1.62.0+dfsg-4+b3 [57.0 kB]
+Get:6 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libboost-iostreams1.62.0 sparc64 1.62.0+dfsg-4+b3 [47.5 kB]
+Get:7 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libsigc++-2.0-0v5 sparc64 2.10.0-1 [59.8 kB]
+Get:8 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libcwidget3v5 sparc64 0.5.17-6 [236 kB]
+Get:9 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 aptitude sparc64 0.8.10-1 [1216 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 4688 kB in 0s (30.4 MB/s)
+Selecting previously unselected package libxapian30:sparc64.
+(Reading database ... 11492 files and directories currently installed.)
+Preparing to unpack .../0-libxapian30_1.4.5-1_sparc64.deb ...
+Unpacking libxapian30:sparc64 (1.4.5-1) ...
+Selecting previously unselected package libsqlite3-0:sparc64.
+Preparing to unpack .../1-libsqlite3-0_3.21.0-1_sparc64.deb ...
+Unpacking libsqlite3-0:sparc64 (3.21.0-1) ...
+Selecting previously unselected package aptitude-common.
+Preparing to unpack .../2-aptitude-common_0.8.10-1_all.deb ...
+Unpacking aptitude-common (0.8.10-1) ...
+Selecting previously unselected package libboost-system1.62.0:sparc64.
+Preparing to unpack .../3-libboost-system1.62.0_1.62.0+dfsg-4+b3_sparc64.deb ...
+Unpacking libboost-system1.62.0:sparc64 (1.62.0+dfsg-4+b3) ...
+Selecting previously unselected package libboost-filesystem1.62.0:sparc64.
+Preparing to unpack .../4-libboost-filesystem1.62.0_1.62.0+dfsg-4+b3_sparc64.deb ...
+Unpacking libboost-filesystem1.62.0:sparc64 (1.62.0+dfsg-4+b3) ...
+Selecting previously unselected package libboost-iostreams1.62.0:sparc64.
+Preparing to unpack .../5-libboost-iostreams1.62.0_1.62.0+dfsg-4+b3_sparc64.deb ...
+Unpacking libboost-iostreams1.62.0:sparc64 (1.62.0+dfsg-4+b3) ...
+Selecting previously unselected package libsigc++-2.0-0v5:sparc64.
+Preparing to unpack .../6-libsigc++-2.0-0v5_2.10.0-1_sparc64.deb ...
+Unpacking libsigc++-2.0-0v5:sparc64 (2.10.0-1) ...
+Selecting previously unselected package libcwidget3v5:sparc64.
+Preparing to unpack .../7-libcwidget3v5_0.5.17-6_sparc64.deb ...
+Unpacking libcwidget3v5:sparc64 (0.5.17-6) ...
+Selecting previously unselected package aptitude.
+Preparing to unpack .../8-aptitude_0.8.10-1_sparc64.deb ...
+Unpacking aptitude (0.8.10-1) ...
+Setting up libxapian30:sparc64 (1.4.5-1) ...
+Setting up aptitude-common (0.8.10-1) ...
+Setting up libboost-iostreams1.62.0:sparc64 (1.62.0+dfsg-4+b3) ...
+Processing triggers for libc-bin (2.25-3) ...
+Setting up libsqlite3-0:sparc64 (3.21.0-1) ...
+Setting up libsigc++-2.0-0v5:sparc64 (2.10.0-1) ...
+Setting up libboost-system1.62.0:sparc64 (1.62.0+dfsg-4+b3) ...
+Setting up libboost-filesystem1.62.0:sparc64 (1.62.0+dfsg-4+b3) ...
+Setting up libcwidget3v5:sparc64 (0.5.17-6) ...
+Setting up aptitude (0.8.10-1) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode
+Processing triggers for libc-bin (2.25-3) ...
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-core-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-core-dummy:sparc64
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+0 packages upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
+Need to get 852 B of archives. After unpacking 0 B will be used.
+Writing extended state information...
+Get: 1 copy:/<<BUILDDIR>>/resolver-8T0hWb/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
+Fetched 852 B in 0s (0 B/s)
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11746 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_sparc64.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+
++------------------------------------------------------------------------------+
+| Check architectures |
++------------------------------------------------------------------------------+
+
+Arch check ok (sparc64 included in any)
+
++------------------------------------------------------------------------------+
+| Install package build dependencies |
++------------------------------------------------------------------------------+
+
+
+Setup apt archive
+-----------------
+
+Merged Build-Depends: binutils (>= 2.27.51.20161118-1sparc64), debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+Filtered Build-Depends: binutils (>= 2.27.51.20161118-1sparc64), debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl
+dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<<BUILDDIR>>/resolver-8T0hWb/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:/<<BUILDDIR>>/resolver-8T0hWb/apt_archive ./ InRelease
+Get:2 copy:/<<BUILDDIR>>/resolver-8T0hWb/apt_archive ./ Release [963 B]
+Ign:3 copy:/<<BUILDDIR>>/resolver-8T0hWb/apt_archive ./ Release.gpg
+Get:4 copy:/<<BUILDDIR>>/resolver-8T0hWb/apt_archive ./ Sources [572 B]
+Get:5 copy:/<<BUILDDIR>>/resolver-8T0hWb/apt_archive ./ Packages [641 B]
+Fetched 2176 B in 0s (76.7 kB/s)
+Reading package lists...
+Reading package lists...
+
++------------------------------------------------------------------------------+
+| Install bcftools build dependencies (aptitude-based resolver) |
++------------------------------------------------------------------------------+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+aptitude is already the newest version (0.8.10-1).
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
+aptitude -y --without-recommends -o Dpkg::Options::=--force-confold -o Aptitude::CmdLine::Ignore-Trust-Violations=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::SolutionCost=safety, priority, non-default-versions -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-bcftools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Level=55000 -o Aptitude::ProblemResolver::Remove-Essential-Level=maximum install sbuild-build-depends-bcftool [...]
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+The following NEW packages will be installed:
+ autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libbz2-dev{a} libcroco3{a} libcurl3-gnutls{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu57{a} libio-pty-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} l [...]
+The following packages are RECOMMENDED but will NOT be installed:
+ bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx-cur publicsuffix shared-mime-info wget xdg-user-dirs
+0 packages upgraded, 56 newly installed, 0 to remove and 2 not upgraded.
+Need to get 24.6 MB of archives. After unpacking 89.7 MB will be used.
+Writing extended state information...
+Get: 1 copy:/<<BUILDDIR>>/resolver-8T0hWb/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [928 B]
+Get: 2 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 groff-base sparc64 1.22.3-9 [1175 kB]
+Get: 3 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libbsd0 sparc64 0.8.6-3 [86.9 kB]
+Get: 4 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libncurses5 sparc64 6.0+20171125-1 [76.4 kB]
+Get: 5 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 bsdmainutils sparc64 9.0.14 [180 kB]
+Get: 6 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libpipeline1 sparc64 1.5.0-1 [24.6 kB]
+Get: 7 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 man-db sparc64 2.7.6.1-4 [1016 kB]
+Get: 8 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libssl1.1 sparc64 1.1.0g-2 [1098 kB]
+Get: 9 http://incoming.ports.debian.org/buildd unstable/main sparc64 libhts2 sparc64 1.5-6 [255 kB]
+Get: 10 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libmagic-mgc sparc64 1:5.32-1 [226 kB]
+Get: 11 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libmagic1 sparc64 1:5.32-1 [103 kB]
+Get: 12 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 file sparc64 1:5.32-1 [63.9 kB]
+Get: 13 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 gettext-base sparc64 0.19.8.1-4 [118 kB]
+Get: 14 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libkeyutils1 sparc64 1.5.9-9.2 [11.9 kB]
+Get: 15 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libkrb5support0 sparc64 1.15.2-2 [58.7 kB]
+Get: 16 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libk5crypto3 sparc64 1.15.2-2 [116 kB]
+Get: 17 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libkrb5-3 sparc64 1.15.2-2 [259 kB]
+Get: 18 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libgssapi-krb5-2 sparc64 1.15.2-2 [129 kB]
+Get: 19 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libsasl2-modules-db sparc64 2.1.27~101-g0780600+dfsg-3 [66.4 kB]
+Get: 20 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libsasl2-2 sparc64 2.1.27~101-g0780600+dfsg-3 [97.6 kB]
+Get: 21 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libldap-common all 2.4.45+dfsg-1 [87.0 kB]
+Get: 22 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libldap-2.4-2 sparc64 2.4.45+dfsg-1 [191 kB]
+Get: 23 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libicu57 sparc64 57.1-8 [7311 kB]
+Get: 24 http://incoming.ports.debian.org/buildd unstable/main sparc64 tabix sparc64 1.5-6 [263 kB]
+Get: 25 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libxml2 sparc64 2.9.4+dfsg1-5.1 [592 kB]
+Get: 26 http://incoming.ports.debian.org/buildd unstable/main sparc64 libhts-dev sparc64 1.5-6 [347 kB]
+Get: 27 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libsigsegv2 sparc64 2.11-1 [29.1 kB]
+Get: 28 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 m4 sparc64 1.4.17-5 [242 kB]
+Get: 29 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 autoconf all 2.69-11 [341 kB]
+Get: 30 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 autotools-dev all 20161112.1+nmu1 [74.2 kB]
+Get: 31 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 automake all 1:1.15.1-3 [736 kB]
+Get: 32 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 autopoint all 0.19.8.1-4 [434 kB]
+Get: 33 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libtool all 2.4.6-2 [545 kB]
+Get: 34 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 dh-autoreconf all 15 [16.2 kB]
+Get: 35 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libarchive-zip-perl all 1.59-1 [95.5 kB]
+Get: 36 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
+Get: 37 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get: 38 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 dh-strip-nondeterminism all 0.040-1 [11.8 kB]
+Get: 39 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libglib2.0-0 sparc64 2.54.2-1 [2588 kB]
+Get: 40 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libcroco3 sparc64 0.6.12-1 [127 kB]
+Get: 41 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 gettext sparc64 0.19.8.1-4 [1228 kB]
+Get: 42 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get: 43 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 po-debconf all 1.0.20 [247 kB]
+Get: 44 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 debhelper all 10.10.9 [975 kB]
+Get: 45 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libbz2-dev sparc64 1.0.6-8.1 [28.9 kB]
+Get: 46 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libnghttp2-14 sparc64 1.28.0-1 [72.0 kB]
+Get: 47 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libpsl5 sparc64 0.19.1-4 [43.6 kB]
+Get: 48 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 librtmp1 sparc64 2.4+20151223.gitfa8646d.1-1 [53.1 kB]
+Get: 49 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libssh2-1 sparc64 1.8.0-1 [125 kB]
+Get: 50 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libcurl3-gnutls sparc64 7.57.0-1 [269 kB]
+Get: 51 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libgslcblas0 sparc64 2.4+dfsg-6 [75.4 kB]
+Get: 52 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libgsl23 sparc64 2.4+dfsg-6 [721 kB]
+Get: 53 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libgsl-dev sparc64 2.4+dfsg-6 [1001 kB]
+Get: 54 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 liblzma-dev sparc64 5.2.2-1.3 [288 kB]
+Get: 55 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 libio-pty-perl sparc64 1:1.08-1.1+b4 [32.7 kB]
+Get: 56 http://ftp.ports.debian.org/debian-ports unstable/main sparc64 zlib1g-dev sparc64 1:1.2.8.dfsg-5 [199 kB]
+Fetched 24.6 MB in 1s (12.9 MB/s)
+debconf: delaying package configuration, since apt-utils is not installed
+Selecting previously unselected package groff-base.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11746 files and directories currently installed.)
+Preparing to unpack .../00-groff-base_1.22.3-9_sparc64.deb ...
+Unpacking groff-base (1.22.3-9) ...
+Selecting previously unselected package libbsd0:sparc64.
+Preparing to unpack .../01-libbsd0_0.8.6-3_sparc64.deb ...
+Unpacking libbsd0:sparc64 (0.8.6-3) ...
+Selecting previously unselected package libncurses5:sparc64.
+Preparing to unpack .../02-libncurses5_6.0+20171125-1_sparc64.deb ...
+Unpacking libncurses5:sparc64 (6.0+20171125-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../03-bsdmainutils_9.0.14_sparc64.deb ...
+Unpacking bsdmainutils (9.0.14) ...
+Selecting previously unselected package libpipeline1:sparc64.
+Preparing to unpack .../04-libpipeline1_1.5.0-1_sparc64.deb ...
+Unpacking libpipeline1:sparc64 (1.5.0-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../05-man-db_2.7.6.1-4_sparc64.deb ...
+Unpacking man-db (2.7.6.1-4) ...
+Selecting previously unselected package libssl1.1:sparc64.
+Preparing to unpack .../06-libssl1.1_1.1.0g-2_sparc64.deb ...
+Unpacking libssl1.1:sparc64 (1.1.0g-2) ...
+Selecting previously unselected package libmagic-mgc.
+Preparing to unpack .../07-libmagic-mgc_1%3a5.32-1_sparc64.deb ...
+Unpacking libmagic-mgc (1:5.32-1) ...
+Selecting previously unselected package libmagic1:sparc64.
+Preparing to unpack .../08-libmagic1_1%3a5.32-1_sparc64.deb ...
+Unpacking libmagic1:sparc64 (1:5.32-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../09-file_1%3a5.32-1_sparc64.deb ...
+Unpacking file (1:5.32-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../10-gettext-base_0.19.8.1-4_sparc64.deb ...
+Unpacking gettext-base (0.19.8.1-4) ...
+Selecting previously unselected package libkeyutils1:sparc64.
+Preparing to unpack .../11-libkeyutils1_1.5.9-9.2_sparc64.deb ...
+Unpacking libkeyutils1:sparc64 (1.5.9-9.2) ...
+Selecting previously unselected package libkrb5support0:sparc64.
+Preparing to unpack .../12-libkrb5support0_1.15.2-2_sparc64.deb ...
+Unpacking libkrb5support0:sparc64 (1.15.2-2) ...
+Selecting previously unselected package libk5crypto3:sparc64.
+Preparing to unpack .../13-libk5crypto3_1.15.2-2_sparc64.deb ...
+Unpacking libk5crypto3:sparc64 (1.15.2-2) ...
+Selecting previously unselected package libkrb5-3:sparc64.
+Preparing to unpack .../14-libkrb5-3_1.15.2-2_sparc64.deb ...
+Unpacking libkrb5-3:sparc64 (1.15.2-2) ...
+Selecting previously unselected package libgssapi-krb5-2:sparc64.
+Preparing to unpack .../15-libgssapi-krb5-2_1.15.2-2_sparc64.deb ...
+Unpacking libgssapi-krb5-2:sparc64 (1.15.2-2) ...
+Selecting previously unselected package libsasl2-modules-db:sparc64.
+Preparing to unpack .../16-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3_sparc64.deb ...
+Unpacking libsasl2-modules-db:sparc64 (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libsasl2-2:sparc64.
+Preparing to unpack .../17-libsasl2-2_2.1.27~101-g0780600+dfsg-3_sparc64.deb ...
+Unpacking libsasl2-2:sparc64 (2.1.27~101-g0780600+dfsg-3) ...
+Selecting previously unselected package libldap-common.
+Preparing to unpack .../18-libldap-common_2.4.45+dfsg-1_all.deb ...
+Unpacking libldap-common (2.4.45+dfsg-1) ...
+Selecting previously unselected package libldap-2.4-2:sparc64.
+Preparing to unpack .../19-libldap-2.4-2_2.4.45+dfsg-1_sparc64.deb ...
+Unpacking libldap-2.4-2:sparc64 (2.4.45+dfsg-1) ...
+Selecting previously unselected package libicu57:sparc64.
+Preparing to unpack .../20-libicu57_57.1-8_sparc64.deb ...
+Unpacking libicu57:sparc64 (57.1-8) ...
+Selecting previously unselected package libxml2:sparc64.
+Preparing to unpack .../21-libxml2_2.9.4+dfsg1-5.1_sparc64.deb ...
+Unpacking libxml2:sparc64 (2.9.4+dfsg1-5.1) ...
+Selecting previously unselected package libsigsegv2:sparc64.
+Preparing to unpack .../22-libsigsegv2_2.11-1_sparc64.deb ...
+Unpacking libsigsegv2:sparc64 (2.11-1) ...
+Selecting previously unselected package m4.
+Preparing to unpack .../23-m4_1.4.17-5_sparc64.deb ...
+Unpacking m4 (1.4.17-5) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../24-autoconf_2.69-11_all.deb ...
+Unpacking autoconf (2.69-11) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../25-autotools-dev_20161112.1+nmu1_all.deb ...
+Unpacking autotools-dev (20161112.1+nmu1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../26-automake_1%3a1.15.1-3_all.deb ...
+Unpacking automake (1:1.15.1-3) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../27-autopoint_0.19.8.1-4_all.deb ...
+Unpacking autopoint (0.19.8.1-4) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../28-libtool_2.4.6-2_all.deb ...
+Unpacking libtool (2.4.6-2) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../29-dh-autoreconf_15_all.deb ...
+Unpacking dh-autoreconf (15) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../30-libarchive-zip-perl_1.59-1_all.deb ...
+Unpacking libarchive-zip-perl (1.59-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../31-libfile-stripnondeterminism-perl_0.040-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.040-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../32-libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../33-dh-strip-nondeterminism_0.040-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.040-1) ...
+Selecting previously unselected package libglib2.0-0:sparc64.
+Preparing to unpack .../34-libglib2.0-0_2.54.2-1_sparc64.deb ...
+Unpacking libglib2.0-0:sparc64 (2.54.2-1) ...
+Selecting previously unselected package libcroco3:sparc64.
+Preparing to unpack .../35-libcroco3_0.6.12-1_sparc64.deb ...
+Unpacking libcroco3:sparc64 (0.6.12-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../36-gettext_0.19.8.1-4_sparc64.deb ...
+Unpacking gettext (0.19.8.1-4) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../37-intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../38-po-debconf_1.0.20_all.deb ...
+Unpacking po-debconf (1.0.20) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../39-debhelper_10.10.9_all.deb ...
+Unpacking debhelper (10.10.9) ...
+Selecting previously unselected package libbz2-dev:sparc64.
+Preparing to unpack .../40-libbz2-dev_1.0.6-8.1_sparc64.deb ...
+Unpacking libbz2-dev:sparc64 (1.0.6-8.1) ...
+Selecting previously unselected package libnghttp2-14:sparc64.
+Preparing to unpack .../41-libnghttp2-14_1.28.0-1_sparc64.deb ...
+Unpacking libnghttp2-14:sparc64 (1.28.0-1) ...
+Selecting previously unselected package libpsl5:sparc64.
+Preparing to unpack .../42-libpsl5_0.19.1-4_sparc64.deb ...
+Unpacking libpsl5:sparc64 (0.19.1-4) ...
+Selecting previously unselected package librtmp1:sparc64.
+Preparing to unpack .../43-librtmp1_2.4+20151223.gitfa8646d.1-1_sparc64.deb ...
+Unpacking librtmp1:sparc64 (2.4+20151223.gitfa8646d.1-1) ...
+Selecting previously unselected package libssh2-1:sparc64.
+Preparing to unpack .../44-libssh2-1_1.8.0-1_sparc64.deb ...
+Unpacking libssh2-1:sparc64 (1.8.0-1) ...
+Selecting previously unselected package libcurl3-gnutls:sparc64.
+Preparing to unpack .../45-libcurl3-gnutls_7.57.0-1_sparc64.deb ...
+Unpacking libcurl3-gnutls:sparc64 (7.57.0-1) ...
+Selecting previously unselected package libgslcblas0:sparc64.
+Preparing to unpack .../46-libgslcblas0_2.4+dfsg-6_sparc64.deb ...
+Unpacking libgslcblas0:sparc64 (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl23:sparc64.
+Preparing to unpack .../47-libgsl23_2.4+dfsg-6_sparc64.deb ...
+Unpacking libgsl23:sparc64 (2.4+dfsg-6) ...
+Selecting previously unselected package libgsl-dev.
+Preparing to unpack .../48-libgsl-dev_2.4+dfsg-6_sparc64.deb ...
+Unpacking libgsl-dev (2.4+dfsg-6) ...
+Selecting previously unselected package libhts2:sparc64.
+Preparing to unpack .../49-libhts2_1.5-6_sparc64.deb ...
+Unpacking libhts2:sparc64 (1.5-6) ...
+Selecting previously unselected package liblzma-dev:sparc64.
+Preparing to unpack .../50-liblzma-dev_5.2.2-1.3_sparc64.deb ...
+Unpacking liblzma-dev:sparc64 (5.2.2-1.3) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../51-tabix_1.5-6_sparc64.deb ...
+Unpacking tabix (1.5-6) ...
+Selecting previously unselected package libhts-dev:sparc64.
+Preparing to unpack .../52-libhts-dev_1.5-6_sparc64.deb ...
+Unpacking libhts-dev:sparc64 (1.5-6) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../53-libio-pty-perl_1%3a1.08-1.1+b4_sparc64.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b4) ...
+Selecting previously unselected package zlib1g-dev:sparc64.
+Preparing to unpack .../54-zlib1g-dev_1%3a1.2.8.dfsg-5_sparc64.deb ...
+Unpacking zlib1g-dev:sparc64 (1:1.2.8.dfsg-5) ...
+Selecting previously unselected package sbuild-build-depends-bcftools-dummy.
+Preparing to unpack .../55-sbuild-build-depends-bcftools-dummy_0.invalid.0_sparc64.deb ...
+Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Setting up libncurses5:sparc64 (6.0+20171125-1) ...
+Setting up libbz2-dev:sparc64 (1.0.6-8.1) ...
+Setting up libarchive-zip-perl (1.59-1) ...
+Setting up libnghttp2-14:sparc64 (1.28.0-1) ...
+Setting up libio-pty-perl (1:1.08-1.1+b4) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libsigsegv2:sparc64 (2.11-1) ...
+Setting up libldap-common (2.4.45+dfsg-1) ...
+Setting up libpsl5:sparc64 (0.19.1-4) ...
+Setting up groff-base (1.22.3-9) ...
+Setting up libglib2.0-0:sparc64 (2.54.2-1) ...
+No schema files found: doing nothing.
+Setting up libsasl2-modules-db:sparc64 (2.1.27~101-g0780600+dfsg-3) ...
+Setting up libsasl2-2:sparc64 (2.1.27~101-g0780600+dfsg-3) ...
+Setting up gettext-base (0.19.8.1-4) ...
+Setting up libpipeline1:sparc64 (1.5.0-1) ...
+Setting up librtmp1:sparc64 (2.4+20151223.gitfa8646d.1-1) ...
+Setting up m4 (1.4.17-5) ...
+Setting up libicu57:sparc64 (57.1-8) ...
+Setting up libbsd0:sparc64 (0.8.6-3) ...
+Setting up libxml2:sparc64 (2.9.4+dfsg1-5.1) ...
+Setting up libmagic-mgc (1:5.32-1) ...
+Setting up libmagic1:sparc64 (1:5.32-1) ...
+Setting up libcroco3:sparc64 (0.6.12-1) ...
+Setting up libssh2-1:sparc64 (1.8.0-1) ...
+Processing triggers for libc-bin (2.25-3) ...
+Setting up autotools-dev (20161112.1+nmu1) ...
+Setting up libldap-2.4-2:sparc64 (2.4.45+dfsg-1) ...
+Setting up libssl1.1:sparc64 (1.1.0g-2) ...
+Setting up liblzma-dev:sparc64 (5.2.2-1.3) ...
+Setting up libkeyutils1:sparc64 (1.5.9-9.2) ...
+Setting up bsdmainutils (9.0.14) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libgslcblas0:sparc64 (2.4+dfsg-6) ...
+Setting up autopoint (0.19.8.1-4) ...
+Setting up zlib1g-dev:sparc64 (1:1.2.8.dfsg-5) ...
+Setting up libfile-stripnondeterminism-perl (0.040-1) ...
+Setting up libgsl23:sparc64 (2.4+dfsg-6) ...
+Setting up gettext (0.19.8.1-4) ...
+Setting up libgsl-dev (2.4+dfsg-6) ...
+Setting up autoconf (2.69-11) ...
+Setting up file (1:5.32-1) ...
+Setting up libkrb5support0:sparc64 (1.15.2-2) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up automake (1:1.15.1-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
+Setting up man-db (2.7.6.1-4) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libtool (2.4.6-2) ...
+Setting up libk5crypto3:sparc64 (1.15.2-2) ...
+Setting up po-debconf (1.0.20) ...
+Setting up libkrb5-3:sparc64 (1.15.2-2) ...
+Setting up libgssapi-krb5-2:sparc64 (1.15.2-2) ...
+Setting up libcurl3-gnutls:sparc64 (7.57.0-1) ...
+Setting up tabix (1.5-6) ...
+Setting up libhts2:sparc64 (1.5-6) ...
+Setting up libhts-dev:sparc64 (1.5-6) ...
+Setting up dh-autoreconf (15) ...
+Setting up dh-strip-nondeterminism (0.040-1) ...
+Setting up debhelper (10.10.9) ...
+Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.25-3) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Building tag database...
+
++------------------------------------------------------------------------------+
+| Build environment |
++------------------------------------------------------------------------------+
+
+Kernel: Linux 4.14.0-1-sparc64-smp sparc64 (sparc64)
+Toolchain package versions: binutils_2.29.1-11 dpkg-dev_1.19.0.4 g++-7_7.2.0-17 gcc-7_7.2.0-17 libc6-dev_2.25-3 libstdc++-7-dev_7.2.0-17 libstdc++6_7.2.0-17 linux-libc-dev_4.14.2-1
+Package versions: adduser_3.116 apt_1.6~alpha5 aptitude_0.8.10-1 aptitude-common_0.8.10-1 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-11 binutils-common_2.29.1-11 binutils-sparc64-linux-gnu_2.29.1-11 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 coreutils_8.28-1 cpp_4:7.2.0-1d1 cpp-7_7.2.0-17 dash_0.5.8-2.5 debconf_1.5.65 debhelper_10.10.9 debian-archiv [...]
+
++------------------------------------------------------------------------------+
+| Build |
++------------------------------------------------------------------------------+
+
+
+Unpack source
+-------------
+
+gpgv: unknown type of key resource 'trustedkeys.kbx'
+gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
+gpgv: Signature made Mon Dec 11 14:53:09 2017 UTC
+gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
+gpgv: issuer "tillea at rki.de"
+gpgv: Can't check signature: No public key
+dpkg-source: warning: failed to verify signature on ./bcftools_1.6-1.dsc
+dpkg-source: info: extracting bcftools in /<<PKGBUILDDIR>>
+dpkg-source: info: unpacking bcftools_1.6.orig.tar.gz
+dpkg-source: info: unpacking bcftools_1.6-1.debian.tar.xz
+dpkg-source: info: applying tests-pluginpath.patch
+dpkg-source: info: applying test-regidx-unsigned-char.patch
+dpkg-source: info: applying fix-test_vcf_query.patch
+
+Check disk space
+----------------
+
+Sufficient free space for build
+
+User Environment
+----------------
+
+APT_CONFIG=/var/lib/sbuild/apt.conf
+DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/113/bus
+DEB_BUILD_OPTIONS=parallel=32
+HOME=/sbuild-nonexistent
+LC_ALL=POSIX
+LOGNAME=buildd4
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=experimental-sparc64-sbuild
+SCHROOT_CHROOT_NAME=experimental-sparc64-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=113
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=experimental-sparc64-sbuild-uXKTic-163911
+SCHROOT_UID=113
+SCHROOT_USER=buildd4
+SHELL=/bin/sh
+USER=buildd4
+XDG_RUNTIME_DIR=/run/user/113
+XDG_SESSION_ID=953
+
+dpkg-buildpackage
+-----------------
+
+dpkg-buildpackage: info: source package bcftools
+dpkg-buildpackage: info: source version 1.6-1
+dpkg-buildpackage: info: source distribution experimental
+ dpkg-source --before-build bcftools-1.6
+dpkg-buildpackage: info: host architecture sparc64
+ fakeroot debian/rules clean
+rm -f config.mk && touch config.mk
+dh clean --parallel
+ dh_auto_clean
+ make -j32 distclean
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+rm -f test/*.o test/*~
+rm -f plugins/*.so plugins/*.P
+rm -rf plugins/*.dSYM
+rm -f gmon.out *.o *~ version.h plugins/*.so plugins/*.P
+rm -rf *.dSYM plugins/*.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 '/<<PKGBUILDDIR>>'
+ dh_clean
+ debian/rules build-arch
+dh build-arch --parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_autoreconf
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+rm -f config.mk && touch config.mk
+export MAKEFLAGS="-s"; dh_autoreconf
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+configure.ac:81: 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:81: the top level
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+dh_auto_configure -- \
+--with-htslib=system \
+--enable-gsl \
+--with-cblas=gslcblas \
+--with-bcf-plugin-dir=/usr/lib/sparc64-linux-gnu/bcftools
+ ./configure --build=sparc64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/sparc64-linux-gnu --libexecdir=\${prefix}/lib/sparc64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/sparc64-linux-gnu/bcftools
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... no
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking shared library type... plain .so
+checking for library containing dlopen... -ldl
+checking if the compiler accepts -rdynamic... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ dh_auto_build -a -O--parallel
+ make -j32
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+echo '#define BCFTOOLS_VERSION "1.6"' > version.h
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/sparc64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl
+gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl
+gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c
+gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl
+gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -ldl -ldl
+gcc -rdynamic -pthread -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 vcfplugin.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 ccall.o em.o prob1.o kmin.o -l [...]
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ dh_auto_test -a -O--parallel
+ make -j32 test VERBOSE=1
+make[1]: Entering directory '/<<PKGBUILDDIR>>'
+./test/test-rbuf
+Inserted 1-9 starting at offset 5:
+ 5 6 7 8 9 0 1 2 3
+ 1 2 3 4 5 6 7 8 9
+4th is 4
+Deleting 1-2:
+ 7 8 9 0 1 2 3
+ 3 4 5 6 7 8 9
+Prepending 0-8:
+ 8 9 0 1 2 3 4 5 6 7
+ 8 7 6 5 4 3 2 1 0 3
+Expanding:
+ 8 9 10 11 12 13 14 15 16 17
+ 8 7 6 5 4 3 2 1 0 3
+./test/test-regidx
+REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix=
+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/KPuGusJkGz/merge.a.vcf.gz 2:3199812-3199812
+.. ok
+
+test_tabix:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/KPuGusJkGz/merge.a.bcf 2:3199812-3199812
+.. ok
+
+test_tabix:
+ tabix /tmp/KPuGusJkGz/merge.a.vcf.gz 1:3000151-3000151
+.. ok
+
+test_tabix:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/KPuGusJkGz/merge.a.bcf 1:3000151-3000151
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/KPuGusJkGz/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/KPuGusJkGz/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/KPuGusJkGz/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/KPuGusJkGz/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/KPuGusJkGz/large_chrom_csi_limit.bcf chr20:1-2147483647
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/KPuGusJkGz/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/KPuGusJkGz/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/KPuGusJkGz/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/KPuGusJkGz/large_chrom_csi_limit.vcf.gz chr20
+.. ok
+
+test_index:
+ /<<PKGBUILDDIR>>/bcftools view -H /tmp/KPuGusJkGz/large_chrom_csi_limit.bcf chr20
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/KPuGusJkGz/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/KPuGusJkGz/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/KPuGusJkGz/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/KPuGusJkGz/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/KPuGusJkGz/idx.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/KPuGusJkGz/idx.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/KPuGusJkGz/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/KPuGusJkGz/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -s /tmp/KPuGusJkGz/empty.bcf
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/KPuGusJkGz/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/KPuGusJkGz/empty.vcf.gz
+.. ok
+
+test_vcf_idxstats:
+ /<<PKGBUILDDIR>>/bcftools index -n /tmp/KPuGusJkGz/empty.bcf
+.. ok
+
+test_vcf_check:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/KPuGusJkGz/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_check_merge:
+ /<<PKGBUILDDIR>>/misc/plot-vcfstats -m /tmp/KPuGusJkGz/check.1.chk /tmp/KPuGusJkGz/check.2.chk /tmp/KPuGusJkGz/check.3.chk /tmp/KPuGusJkGz/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/KPuGusJkGz/stats.a.vcf.gz /tmp/KPuGusJkGz/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s B /tmp/KPuGusJkGz/stats.a.vcf.gz /tmp/KPuGusJkGz/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_stats:
+ /<<PKGBUILDDIR>>/bcftools stats -s - /tmp/KPuGusJkGz/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID '
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 /tmp/KPuGusJkGz/isec.a.vcf.gz /tmp/KPuGusJkGz/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 /tmp/KPuGusJkGz/isec.a.vcf.gz /tmp/KPuGusJkGz/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/KPuGusJkGz/isec.a.vcf.gz /tmp/KPuGusJkGz/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/KPuGusJkGz/isec.a.vcf.gz /tmp/KPuGusJkGz/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -c both /tmp/KPuGusJkGz/isec.a.vcf.gz /tmp/KPuGusJkGz/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -c both /tmp/KPuGusJkGz/isec.a.vcf.gz /tmp/KPuGusJkGz/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -n =2 -c any /tmp/KPuGusJkGz/isec.a.vcf.gz /tmp/KPuGusJkGz/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -n =2 -c any /tmp/KPuGusJkGz/isec.a.vcf.gz /tmp/KPuGusJkGz/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -C -c any /tmp/KPuGusJkGz/isec.a.vcf.gz /tmp/KPuGusJkGz/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -C -c any /tmp/KPuGusJkGz/isec.a.vcf.gz /tmp/KPuGusJkGz/isec.b.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_isec2:
+ /<<PKGBUILDDIR>>/bcftools isec --no-version -T /tmp/KPuGusJkGz/isec.tab.gz /tmp/KPuGusJkGz/isec.a.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/isec.tab.out
+ /<<PKGBUILDDIR>>/test/isec.tab.out.new
+.. failed ...
+
+test_vcf_isec2:
+ /<<PKGBUILDDIR>>/bcftools isec -Ob -T /tmp/KPuGusJkGz/isec.tab.gz /tmp/KPuGusJkGz/isec.a.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/isec.tab.out
+ /<<PKGBUILDDIR>>/test/isec.tab.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples /tmp/KPuGusJkGz/merge.a.vcf.gz /tmp/KPuGusJkGz/merge.b.vcf.gz /tmp/KPuGusJkGz/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.out
+ /<<PKGBUILDDIR>>/test/merge.abc.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples /tmp/KPuGusJkGz/merge.a.vcf.gz /tmp/KPuGusJkGz/merge.b.vcf.gz /tmp/KPuGusJkGz/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -Fx /tmp/KPuGusJkGz/merge.a.vcf.gz /tmp/KPuGusJkGz/merge.b.vcf.gz /tmp/KPuGusJkGz/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out
+ /<<PKGBUILDDIR>>/test/merge.abc.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -Fx /tmp/KPuGusJkGz/merge.a.vcf.gz /tmp/KPuGusJkGz/merge.b.vcf.gz /tmp/KPuGusJkGz/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -0 /tmp/KPuGusJkGz/merge.a.vcf.gz /tmp/KPuGusJkGz/merge.b.vcf.gz /tmp/KPuGusJkGz/merge.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out
+ /<<PKGBUILDDIR>>/test/merge.abc.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -0 /tmp/KPuGusJkGz/merge.a.vcf.gz /tmp/KPuGusJkGz/merge.b.vcf.gz /tmp/KPuGusJkGz/merge.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m none /tmp/KPuGusJkGz/merge.2.a.vcf.gz /tmp/KPuGusJkGz/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.none.out
+ /<<PKGBUILDDIR>>/test/merge.2.none.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m none /tmp/KPuGusJkGz/merge.2.a.vcf.gz /tmp/KPuGusJkGz/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m both /tmp/KPuGusJkGz/merge.2.a.vcf.gz /tmp/KPuGusJkGz/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.both.out
+ /<<PKGBUILDDIR>>/test/merge.2.both.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m both /tmp/KPuGusJkGz/merge.2.a.vcf.gz /tmp/KPuGusJkGz/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m all /tmp/KPuGusJkGz/merge.2.a.vcf.gz /tmp/KPuGusJkGz/merge.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.2.all.out
+ /<<PKGBUILDDIR>>/test/merge.2.all.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m all /tmp/KPuGusJkGz/merge.2.a.vcf.gz /tmp/KPuGusJkGz/merge.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/KPuGusJkGz/merge.3.a.vcf.gz /tmp/KPuGusJkGz/merge.3.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.3.out
+ /<<PKGBUILDDIR>>/test/merge.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/KPuGusJkGz/merge.3.a.vcf.gz /tmp/KPuGusJkGz/merge.3.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.3.out
+ /<<PKGBUILDDIR>>/test/merge.3.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --force-samples -m id /tmp/KPuGusJkGz/merge.4.a.vcf.gz /tmp/KPuGusJkGz/merge.4.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.4.out
+ /<<PKGBUILDDIR>>/test/merge.4.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --force-samples -m id /tmp/KPuGusJkGz/merge.4.a.vcf.gz /tmp/KPuGusJkGz/merge.4.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - /tmp/KPuGusJkGz/gvcf.merge.1.vcf.gz /tmp/KPuGusJkGz/gvcf.merge.2.vcf.gz /tmp/KPuGusJkGz/gvcf.merge.3.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - /tmp/KPuGusJkGz/gvcf.merge.1.vcf.gz /tmp/KPuGusJkGz/gvcf.merge.2.vcf.gz /tmp/KPuGusJkGz/gvcf.merge.3.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out
+ /<<PKGBUILDDIR>>/test/gvcf.merge.1.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - /tmp/KPuGusJkGz/merge.gvcf.2.a.vcf.gz /tmp/KPuGusJkGz/merge.gvcf.2.b.vcf.gz /tmp/KPuGusJkGz/merge.gvcf.2.c.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - /tmp/KPuGusJkGz/merge.gvcf.2.a.vcf.gz /tmp/KPuGusJkGz/merge.gvcf.2.b.vcf.gz /tmp/KPuGusJkGz/merge.gvcf.2.c.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out
+ /<<PKGBUILDDIR>>/test/merge.gvcf.2.out.new
+.. failed ...
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version --gvcf - -i SRC:join /tmp/KPuGusJkGz/merge.gvcf.3.a.vcf.gz /tmp/KPuGusJkGz/merge.gvcf.3.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/KPuGusJkGz/merge.gvcf.3.a.vcf.gz /tmp/KPuGusJkGz/merge.gvcf.3.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge --no-version /tmp/KPuGusJkGz/merge.5.a.vcf.gz /tmp/KPuGusJkGz/merge.5.b.vcf.gz
+.. ok
+
+test_vcf_merge:
+ /<<PKGBUILDDIR>>/bcftools merge -Ob /tmp/KPuGusJkGz/merge.5.a.vcf.gz /tmp/KPuGusJkGz/merge.5.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/KPuGusJkGz/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XRI\n' -i'XRI[*]>1111'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' /tmp/KPuGusJkGz/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/KPuGusJkGz/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/KPuGusJkGz/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10' /tmp/KPuGusJkGz/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/KPuGusJkGz/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/KPuGusJkGz/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/KPuGusJkGz/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/KPuGusJkGz/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/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/KPuGusJkGz/view.vectors.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/query.12.out
+ /<<PKGBUILDDIR>>/test/query.12.out.new
+.. failed ...
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/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'
+/bin/bash: line 1: 178867 Done /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.vectors.vcf.gz
+ 178868 Bus error | /<<PKGBUILDDIR>>/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'
+
+ Non-zero status 138
+.. failed ...
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' /tmp/KPuGusJkGz/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' /tmp/KPuGusJkGz/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' /tmp/KPuGusJkGz/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' /tmp/KPuGusJkGz/query.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/KPuGusJkGz/query.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IINT!="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IINT="."' -f'%POS %IINT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%LINE' /tmp/KPuGusJkGz/query.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%LINE'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/KPuGusJkGz/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/KPuGusJkGz/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/KPuGusJkGz/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/KPuGusJkGz/query.filter-type.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.filter-type.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/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/KPuGusJkGz/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/filter-missing-floats.vcf.gz | /<<PKGBUILDDIR>>/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:
+ /<<PKGBUILDDIR>>/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/KPuGusJkGz/filter-missing-floats.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/filter-missing-floats.vcf.gz | /<<PKGBUILDDIR>>/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:
+ /<<PKGBUILDDIR>>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/KPuGusJkGz/missing.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/missing.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/KPuGusJkGz/query.filter.2.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/query.filter.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGS]\n' -i'FGS[1-2,4]="EE"'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGI]\n' -i'FGI[1-2,5]=6'
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_query:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.filter.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%POS[ %FGF]\n' -i'FGF[1-3,4]=5e-5'
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -cx -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/KPuGusJkGz/norm.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.out
+ /<<PKGBUILDDIR>>/test/norm.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -cx -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/KPuGusJkGz/norm.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.out
+ /<<PKGBUILDDIR>>/test/norm.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- /tmp/KPuGusJkGz/norm.split.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.split.out
+ /<<PKGBUILDDIR>>/test/norm.split.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- /tmp/KPuGusJkGz/norm.split.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.split.out
+ /<<PKGBUILDDIR>>/test/norm.split.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- /tmp/KPuGusJkGz/norm.split.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- /tmp/KPuGusJkGz/norm.split.2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m- -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/KPuGusJkGz/norm.split.vcf.gz 2>/dev/null
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m- -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/KPuGusJkGz/norm.split.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/KPuGusJkGz/norm.merge.vcf.gz 2>/dev/null
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/KPuGusJkGz/norm.merge.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.out
+ /<<PKGBUILDDIR>>/test/norm.merge.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/KPuGusJkGz/norm.merge.2.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/KPuGusJkGz/norm.merge.2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ /tmp/KPuGusJkGz/norm.merge.3.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ /tmp/KPuGusJkGz/norm.merge.3.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.'
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -m+ -s /tmp/KPuGusJkGz/norm.merge.vcf.gz 2>/dev/null
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -m+ -s /tmp/KPuGusJkGz/norm.merge.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out
+ /<<PKGBUILDDIR>>/test/norm.merge.strict.out.new
+.. failed ...
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -Nc s -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/KPuGusJkGz/norm.setref.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -Nc s -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/KPuGusJkGz/norm.setref.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm --no-version -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/KPuGusJkGz/norm.telomere.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_norm:
+ /<<PKGBUILDDIR>>/bcftools norm -Ob -f /<<PKGBUILDDIR>>/test/norm.fa /tmp/KPuGusJkGz/norm.telomere.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/KPuGusJkGz/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.1.out
+ /<<PKGBUILDDIR>>/test/view.1.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/KPuGusJkGz/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.1.out
+ /<<PKGBUILDDIR>>/test/view.1.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/KPuGusJkGz/view.vcf.gz -r20,Y
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.2.out
+ /<<PKGBUILDDIR>>/test/view.2.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/KPuGusJkGz/view.vcf.gz -r20,Y | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.2.out
+ /<<PKGBUILDDIR>>/test/view.2.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -xs NA00003 /tmp/KPuGusJkGz/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.3.out
+ /<<PKGBUILDDIR>>/test/view.3.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -xs NA00003 /tmp/KPuGusJkGz/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.3.out
+ /<<PKGBUILDDIR>>/test/view.3.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/KPuGusJkGz/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.4.out
+ /<<PKGBUILDDIR>>/test/view.4.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/KPuGusJkGz/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.4.out
+ /<<PKGBUILDDIR>>/test/view.4.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -p /tmp/KPuGusJkGz/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.5.out
+ /<<PKGBUILDDIR>>/test/view.5.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -p /tmp/KPuGusJkGz/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.5.out
+ /<<PKGBUILDDIR>>/test/view.5.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -P /tmp/KPuGusJkGz/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.6.out
+ /<<PKGBUILDDIR>>/test/view.6.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -P /tmp/KPuGusJkGz/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.6.out
+ /<<PKGBUILDDIR>>/test/view.6.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/KPuGusJkGz/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/KPuGusJkGz/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -Hu /tmp/KPuGusJkGz/view.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -GVsnps /tmp/KPuGusJkGz/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.9.out
+ /<<PKGBUILDDIR>>/test/view.9.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -GVsnps /tmp/KPuGusJkGz/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.9.out
+ /<<PKGBUILDDIR>>/test/view.9.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/KPuGusJkGz/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.10.out
+ /<<PKGBUILDDIR>>/test/view.10.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/KPuGusJkGz/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -s ^NA00003 /tmp/KPuGusJkGz/view.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.exclude.out
+ /<<PKGBUILDDIR>>/test/view.exclude.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -s ^NA00003 /tmp/KPuGusJkGz/view.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.exclude.out
+ /<<PKGBUILDDIR>>/test/view.exclude.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version /tmp/KPuGusJkGz/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/view.omitgenotypes.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -G /tmp/KPuGusJkGz/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -G /tmp/KPuGusJkGz/view.omitgenotypes.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -HG /tmp/KPuGusJkGz/view.omitgenotypes.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -a /tmp/KPuGusJkGz/many.alleles.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -a /tmp/KPuGusJkGz/many.alleles.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asA /tmp/KPuGusJkGz/view.vectors.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asA /tmp/KPuGusJkGz/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out
+ /<<PKGBUILDDIR>>/test/view.vectors.A.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asB /tmp/KPuGusJkGz/view.vectors.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asB /tmp/KPuGusJkGz/view.vectors.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out
+ /<<PKGBUILDDIR>>/test/view.vectors.B.out.new
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -asA /tmp/KPuGusJkGz/view.vectors.2.vcf.gz
+[E::bcf_remove_allele_set] Unexpected number of values in INFO/IAF at 1:10; expected Number=A=2, but found 1
+Error: Could not trim alleles at 1:10
+
+ Non-zero status 255
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -asA /tmp/KPuGusJkGz/view.vectors.2.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[E::bcf_remove_allele_set] Unexpected number of values in INFO/IAF at 1:10; expected Number=A=2, but found 1
+Error: Could not trim alleles at 1:10
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[0]="AAAAAA"' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[2]="C"' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FGS[4]="EE"' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'FMT/FRS[1]="BB"' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i'TXT0="text"' /tmp/KPuGusJkGz/view.filter.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -T /<<PKGBUILDDIR>>/test/view.chrs.tab /tmp/KPuGusJkGz/view.chrs.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -i 'POS>=3062917' /tmp/KPuGusJkGz/filter.2.vcf.gz 1:3062917-3157410
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view -Ob -i 'POS>=3062917' /tmp/KPuGusJkGz/filter.2.vcf.gz 1:3062917-3157410 | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'TXT0="text"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'TXT0="text"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FRS[1]="BB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FRS[1]="BB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[0]="AAAAAA"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[0]="AAAAAA"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[1]="BBB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[1]="BBB"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/FGS[4]="EE"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/FGS[4]="EE"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S. -e'FMT/STR="XX"' /<<PKGBUILDDIR>>/test/view.filter.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S. -e'FMT/STR="XX"' /<<PKGBUILDDIR>>/test/view.filter.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -C5:nonmajor /tmp/KPuGusJkGz/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -c6:nonmajor /tmp/KPuGusJkGz/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -q0.3:major /tmp/KPuGusJkGz/view.minmaxac.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/KPuGusJkGz/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/KPuGusJkGz/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_view:
+ /<<PKGBUILDDIR>>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/KPuGusJkGz/view.filter.annovar.vcf.gz
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mg0 /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup.2.out
+ /<<PKGBUILDDIR>>/test/mpileup.2.out.new
+.. failed ...
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mg0 /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup.2.out
+ /<<PKGBUILDDIR>>/test/mpileup.2.out.new
+.. failed ...
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call_cAls:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -mA -C alleles -T /tmp/KPuGusJkGz/mpileup.tab.gz /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null
+.. ok
+
+test_vcf_call_cAls:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -mA -C alleles -T /tmp/KPuGusJkGz/mpileup.tab.gz /<<PKGBUILDDIR>>/test/mpileup.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv /<<PKGBUILDDIR>>/test/mpileup.c.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv /<<PKGBUILDDIR>>/test/mpileup.c.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.ped /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call --no-version -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null
+.. ok
+
+test_vcf_call:
+ /<<PKGBUILDDIR>>/bcftools call -Ob -cv --ploidy-file /<<PKGBUILDDIR>>/test/mpileup.ploidy -S /<<PKGBUILDDIR>>/test/mpileup.2.samples /<<PKGBUILDDIR>>/test/mpileup.c.X.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -mx -g2 -G2 /<<PKGBUILDDIR>>/test/filter.1.vcf | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/filter.1.out
+ /<<PKGBUILDDIR>>/test/filter.1.out.new
+.. failed ...
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -mx -g2 -G2 /<<PKGBUILDDIR>>/test/filter.1.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/filter.1.out
+ /<<PKGBUILDDIR>>/test/filter.1.out.new
+.. failed ...
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<<PKGBUILDDIR>>/test/filter.2.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'DP=19' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'DP=19' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /<<PKGBUILDDIR>>/test/filter.3.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'ALT="."' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'ALT="."' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS\t%AC[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S . -i 'FORMAT/TEST3<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -S . -i 'FORMAT/TEST4<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /<<PKGBUILDDIR>>/test/filter.4.vcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="A"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="A"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="RR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="RR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="RA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="RA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="AR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="AR"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="AA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="AA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="aA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="aA"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="Aa"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="Aa"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HOM"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HOM"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HET"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HET"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -i'GT="HAP"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_filter:
+ /<<PKGBUILDDIR>>/bcftools filter -Ob -i'GT="HAP"' /<<PKGBUILDDIR>>/test/filter.2.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%POS[\t%GT]\n'
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -m 0 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.UX7YkM
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -Ob -m 0 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.qONEis
+Merging 15 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -m 1000 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.hRu2Ge
+Merging 4 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_sort:
+ /<<PKGBUILDDIR>>/bcftools sort -Ob -m 1000 /<<PKGBUILDDIR>>/test/sort.vcf | /<<PKGBUILDDIR>>/bcftools view | /<<PKGBUILDDIR>>/bcftools query -f '%CHROM\t%POS\n'
+Writing to /tmp/bcftools-sort.LCVI2z
+Merging 4 temporary files
+Cleaning
+Done
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<<PKGBUILDDIR>>/test/regions.tab /tmp/KPuGusJkGz/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<<PKGBUILDDIR>>/test/regions.tab
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /<<PKGBUILDDIR>>/test/regions.tab /tmp/KPuGusJkGz/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/KPuGusJkGz/regions.tab.gz /tmp/KPuGusJkGz/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/KPuGusJkGz/regions.tab.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/KPuGusJkGz/regions.tab.gz /tmp/KPuGusJkGz/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/KPuGusJkGz/regions.bed /tmp/KPuGusJkGz/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/KPuGusJkGz/regions.bed
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/KPuGusJkGz/regions.bed /tmp/KPuGusJkGz/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/KPuGusJkGz/regions.bed.gz /tmp/KPuGusJkGz/regions.vcf.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/regions.vcf.gz | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/KPuGusJkGz/regions.bed.gz
+.. ok
+
+test_vcf_regions:
+ /<<PKGBUILDDIR>>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/KPuGusJkGz/regions.bed.gz /tmp/KPuGusJkGz/regions.vcf.gz
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/KPuGusJkGz/annotate.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/KPuGusJkGz/annotate.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/KPuGusJkGz/annotate2.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/KPuGusJkGz/annotate2.tab.gz -h /<<PKGBUILDDIR>>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<<PKGBUILDDIR>>/test/annotate.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/KPuGusJkGz/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/KPuGusJkGz/annotate.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/KPuGusJkGz/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/KPuGusJkGz/annotate.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/KPuGusJkGz/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/KPuGusJkGz/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/KPuGusJkGz/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/KPuGusJkGz/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/KPuGusJkGz/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/KPuGusJkGz/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/KPuGusJkGz/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/KPuGusJkGz/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -x FORMAT /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -x FORMAT /<<PKGBUILDDIR>>/test/annotate3.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/KPuGusJkGz/annots4.vcf.gz -c +INFO /tmp/KPuGusJkGz/annotate4.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/KPuGusJkGz/annots4.vcf.gz -c +INFO /tmp/KPuGusJkGz/annotate4.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/KPuGusJkGz/annots4.tab.gz -h /<<PKGBUILDDIR>>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<<PKGBUILDDIR>>/test/annotate4.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/KPuGusJkGz/annots4.tab.gz -h /<<PKGBUILDDIR>>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<<PKGBUILDDIR>>/test/annotate4.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/KPuGusJkGz/annots10.tab.gz -h /<<PKGBUILDDIR>>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<<PKGBUILDDIR>>/test/annotate10.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/KPuGusJkGz/annots10.tab.gz -h /<<PKGBUILDDIR>>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<<PKGBUILDDIR>>/test/annotate10.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/KPuGusJkGz/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/KPuGusJkGz/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/KPuGusJkGz/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/KPuGusJkGz/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/KPuGusJkGz/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<<PKGBUILDDIR>>/test/annotate2.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/KPuGusJkGz/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<<PKGBUILDDIR>>/test/annotate2.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/KPuGusJkGz/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/KPuGusJkGz/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/KPuGusJkGz/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/KPuGusJkGz/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/KPuGusJkGz/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/KPuGusJkGz/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/KPuGusJkGz/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/KPuGusJkGz/annotate2.vcf.gz 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +missing2ref --no-version /tmp/KPuGusJkGz/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +missing2ref --no-version /tmp/KPuGusJkGz/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/KPuGusJkGz/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/KPuGusJkGz/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/KPuGusJkGz/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +setGT --no-version /tmp/KPuGusJkGz/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -a /tmp/KPuGusJkGz/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<<PKGBUILDDIR>>/test/annotate9.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_annotate:
+ /<<PKGBUILDDIR>>/bcftools annotate -Ob -a /tmp/KPuGusJkGz/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<<PKGBUILDDIR>>/test/annotate9.vcf 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-AN-AC --no-version /tmp/KPuGusJkGz/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-AN-AC --no-version /tmp/KPuGusJkGz/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +dosage /tmp/KPuGusJkGz/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +dosage /tmp/KPuGusJkGz/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixploidy --no-version /tmp/KPuGusJkGz/fixploidy.vcf.gz -- -s /<<PKGBUILDDIR>>/test/fixploidy.samples -p /<<PKGBUILDDIR>>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixploidy --no-version /tmp/KPuGusJkGz/fixploidy.bcf -- -s /<<PKGBUILDDIR>>/test/fixploidy.samples -p /<<PKGBUILDDIR>>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/KPuGusJkGz/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/KPuGusJkGz/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/KPuGusJkGz/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +guess-ploidy /tmp/KPuGusJkGz/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+Warning: PL tag not found in header, switching to GL
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/KPuGusJkGz/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/KPuGusJkGz/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/KPuGusJkGz/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +tag2tag --no-version /tmp/KPuGusJkGz/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/KPuGusJkGz/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/KPuGusJkGz/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/KPuGusJkGz/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/KPuGusJkGz/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out
+ /<<PKGBUILDDIR>>/test/fill-tags.2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/KPuGusJkGz/view.vcf.gz -- -t AC -S /<<PKGBUILDDIR>>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/KPuGusJkGz/view.bcf -- -t AC -S /<<PKGBUILDDIR>>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out
+ /<<PKGBUILDDIR>>/test/fill-tags.3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/KPuGusJkGz/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/KPuGusJkGz/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/KPuGusJkGz/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-tags --no-version /tmp/KPuGusJkGz/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTisec /tmp/KPuGusJkGz/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +trio-switch-rate /tmp/KPuGusJkGz/trio.vcf.gz -- -p /<<PKGBUILDDIR>>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +trio-switch-rate /tmp/KPuGusJkGz/trio.bcf -- -p /<<PKGBUILDDIR>>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +ad-bias /tmp/KPuGusJkGz/ad-bias.vcf.gz -- -s /<<PKGBUILDDIR>>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +ad-bias /tmp/KPuGusJkGz/ad-bias.bcf -- -s /<<PKGBUILDDIR>>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +af-dist /tmp/KPuGusJkGz/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +af-dist /tmp/KPuGusJkGz/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixref /tmp/KPuGusJkGz/fixref.2a.vcf.gz -- -f /<<PKGBUILDDIR>>/test/norm.fa -i /tmp/KPuGusJkGz/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fixref /tmp/KPuGusJkGz/fixref.2a.bcf -- -f /<<PKGBUILDDIR>>/test/norm.fa -i /tmp/KPuGusJkGz/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/KPuGusJkGz/aa.vcf.gz -- -f /<<PKGBUILDDIR>>/test/aa.fa -c AA -h /<<PKGBUILDDIR>>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/aa.out
+ /<<PKGBUILDDIR>>/test/aa.out.new
+.. failed ...
+
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/KPuGusJkGz/aa.bcf -- -f /<<PKGBUILDDIR>>/test/aa.fa -c AA -h /<<PKGBUILDDIR>>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/aa.out
+ /<<PKGBUILDDIR>>/test/aa.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/KPuGusJkGz/ref.vcf.gz -- -f /<<PKGBUILDDIR>>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+
+ Non-zero status 1
+.. failed ...
+
+[E::bcf_record_check] Bad BCF record - shared section malformed or too short
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +fill-from-fasta /tmp/KPuGusJkGz/ref.bcf -- -f /<<PKGBUILDDIR>>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/ref.out
+ /<<PKGBUILDDIR>>/test/ref.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/KPuGusJkGz/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/KPuGusJkGz/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/KPuGusJkGz/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/KPuGusJkGz/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/KPuGusJkGz/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +GTsubset --no-version /tmp/KPuGusJkGz/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out
+ /<<PKGBUILDDIR>>/test/view.GTsubset.NA1NA2NA3.out.new
+.. failed ...
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/KPuGusJkGz/mendelian.vcf.gz -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/KPuGusJkGz/mendelian.bcf -- -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/KPuGusJkGz/mendelian.vcf.gz -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/KPuGusJkGz/mendelian.bcf -- -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/KPuGusJkGz/mendelian.vcf.gz -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_plugin:
+ /<<PKGBUILDDIR>>/bcftools +mendelian --no-version /tmp/KPuGusJkGz/mendelian.bcf -- -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version /tmp/KPuGusJkGz/concat.1.a.vcf.gz /tmp/KPuGusJkGz/concat.1.b.vcf.gz
+.. ok
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob /tmp/KPuGusJkGz/concat.1.a.vcf.gz /tmp/KPuGusJkGz/concat.1.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.1.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.1.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version /tmp/KPuGusJkGz/concat.1.a.bcf /tmp/KPuGusJkGz/concat.1.b.bcf
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob /tmp/KPuGusJkGz/concat.1.a.bcf /tmp/KPuGusJkGz/concat.1.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.1.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -a /tmp/KPuGusJkGz/concat.2.a.vcf.gz /tmp/KPuGusJkGz/concat.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -a /tmp/KPuGusJkGz/concat.2.a.vcf.gz /tmp/KPuGusJkGz/concat.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -a /tmp/KPuGusJkGz/concat.2.a.bcf /tmp/KPuGusJkGz/concat.2.b.bcf
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -a /tmp/KPuGusJkGz/concat.2.a.bcf /tmp/KPuGusJkGz/concat.2.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.2.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -aD /tmp/KPuGusJkGz/concat.2.a.vcf.gz /tmp/KPuGusJkGz/concat.2.b.vcf.gz
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -aD /tmp/KPuGusJkGz/concat.2.a.vcf.gz /tmp/KPuGusJkGz/concat.2.b.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -aD /tmp/KPuGusJkGz/concat.2.a.bcf /tmp/KPuGusJkGz/concat.2.b.bcf
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -aD /tmp/KPuGusJkGz/concat.2.a.bcf /tmp/KPuGusJkGz/concat.2.b.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.4.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -l /tmp/KPuGusJkGz/concat.3.a.vcf.gz /tmp/KPuGusJkGz/concat.3.b.vcf.gz /tmp/KPuGusJkGz/concat.3.0.vcf.gz /tmp/KPuGusJkGz/concat.3.c.vcf.gz /tmp/KPuGusJkGz/concat.3.d.vcf.gz /tmp/KPuGusJkGz/concat.3.e.vcf.gz /tmp/KPuGusJkGz/concat.3.f.vcf.gz
+[E::vcf_format] Invalid BCF, the FORMAT tag id=-13056 not present in the header
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.vcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -l /tmp/KPuGusJkGz/concat.3.a.vcf.gz /tmp/KPuGusJkGz/concat.3.b.vcf.gz /tmp/KPuGusJkGz/concat.3.0.vcf.gz /tmp/KPuGusJkGz/concat.3.c.vcf.gz /tmp/KPuGusJkGz/concat.3.d.vcf.gz /tmp/KPuGusJkGz/concat.3.e.vcf.gz /tmp/KPuGusJkGz/concat.3.f.vcf.gz | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+Failed to open -: unknown file type
+
+ Non-zero status 1
+.. failed ...
+
+[W::bcf_record_check] Bad BCF record: Invalid INFO id -14336
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --no-version -l /tmp/KPuGusJkGz/concat.3.a.bcf /tmp/KPuGusJkGz/concat.3.b.bcf /tmp/KPuGusJkGz/concat.3.0.bcf /tmp/KPuGusJkGz/concat.3.c.bcf /tmp/KPuGusJkGz/concat.3.d.bcf /tmp/KPuGusJkGz/concat.3.e.bcf /tmp/KPuGusJkGz/concat.3.f.bcf
+[W::bcf_record_check] Bad BCF record: Invalid INFO id -14336
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080
+[E::vcf_format] Invalid BCF, the FORMAT tag id=-13056 not present in the header
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out.new
+.. failed ...
+
+test_vcf_concat:
+ /<<PKGBUILDDIR>>/bcftools concat -Ob -l /tmp/KPuGusJkGz/concat.3.a.bcf /tmp/KPuGusJkGz/concat.3.b.bcf /tmp/KPuGusJkGz/concat.3.0.bcf /tmp/KPuGusJkGz/concat.3.c.bcf /tmp/KPuGusJkGz/concat.3.d.bcf /tmp/KPuGusJkGz/concat.3.e.bcf /tmp/KPuGusJkGz/concat.3.f.bcf | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+[W::bcf_record_check] Bad BCF record: Invalid INFO id -14336
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080
+[W::bcf_record_check] Bad BCF record: Invalid FORMAT id -13056
+Random seed for test_naive_concat: 2634718377
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out
+ /<<PKGBUILDDIR>>/test/concat.3.bcf.out.new
+.. failed ...
+
+test_naive_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --naive /tmp/KPuGusJkGz/naive_concat.0.bcf /tmp/KPuGusJkGz/naive_concat.1.bcf /tmp/KPuGusJkGz/naive_concat.2.bcf /tmp/KPuGusJkGz/naive_concat.3.bcf /tmp/KPuGusJkGz/naive_concat.4.bcf /tmp/KPuGusJkGz/naive_concat.5.bcf /tmp/KPuGusJkGz/naive_concat.6.bcf /tmp/KPuGusJkGz/naive_concat.7.bcf /tmp/KPuGusJkGz/naive_concat.8.bcf /tmp/KPuGusJkGz/naive_concat.9.bcf | /<<PKGBUILDDIR>>/bcftools view -H
+[E::hts_realloc_or_die] Cannot allocate memory
+Failed to open -: unknown file type
+
+ Non-zero status 255
+.. failed ...
+
+test_naive_concat:
+ /<<PKGBUILDDIR>>/bcftools concat --naive /tmp/KPuGusJkGz/naive_concat.0.vcf.gz /tmp/KPuGusJkGz/naive_concat.1.vcf.gz /tmp/KPuGusJkGz/naive_concat.2.vcf.gz /tmp/KPuGusJkGz/naive_concat.3.vcf.gz /tmp/KPuGusJkGz/naive_concat.4.vcf.gz /tmp/KPuGusJkGz/naive_concat.5.vcf.gz /tmp/KPuGusJkGz/naive_concat.6.vcf.gz /tmp/KPuGusJkGz/naive_concat.7.vcf.gz /tmp/KPuGusJkGz/naive_concat.8.vcf.gz /tmp/KPuGusJkGz/naive_concat.9.vcf.gz | /<<PKGBUILDDIR>>/bcftools view -H
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/concat.naive.vcf.out
+ /<<PKGBUILDDIR>>/test/concat.naive.vcf.out.new
+.. failed ...
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /tmp/KPuGusJkGz/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/KPuGusJkGz/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr /tmp/KPuGusJkGz/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/KPuGusJkGz/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /tmp/KPuGusJkGz/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/KPuGusJkGz/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples /tmp/KPuGusJkGz/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/KPuGusJkGz/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /tmp/KPuGusJkGz/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/KPuGusJkGz/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 /tmp/KPuGusJkGz/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/KPuGusJkGz/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples2 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /tmp/KPuGusJkGz/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/KPuGusJkGz/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 /tmp/KPuGusJkGz/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/KPuGusJkGz/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples3 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/reheader.vcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /tmp/KPuGusJkGz/reheader.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/KPuGusJkGz/reheader.bcf | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 /tmp/KPuGusJkGz/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/KPuGusJkGz/reheader.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -s /<<PKGBUILDDIR>>/test/reheader.samples4 | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /<<PKGBUILDDIR>>/test/empty.vcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /<<PKGBUILDDIR>>/test/empty.vcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /tmp/KPuGusJkGz/empty.bcf | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/KPuGusJkGz/empty.bcf | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr /tmp/KPuGusJkGz/empty.vcf.gz | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_vcf_reheader:
+ cat /tmp/KPuGusJkGz/empty.vcf.gz | /<<PKGBUILDDIR>>/bcftools reheader -h /<<PKGBUILDDIR>>/test/reheader.empty.hdr | /<<PKGBUILDDIR>>/bcftools view --no-version
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/KPuGusJkGz/rename.map -Ov /tmp/KPuGusJkGz/annotate.bcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/KPuGusJkGz/rename.map -Ob /tmp/KPuGusJkGz/annotate.bcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/KPuGusJkGz/rename.map -Ov /<<PKGBUILDDIR>>/test/annotate.vcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_rename_chrs:
+ /<<PKGBUILDDIR>>/bcftools annotate --rename-chrs /tmp/KPuGusJkGz/rename.map -Ob /<<PKGBUILDDIR>>/test/annotate.vcf | /<<PKGBUILDDIR>>/bcftools query -f'%CHROM\t%POS\n'
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. /tmp/KPuGusJkGz/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- /tmp/KPuGusJkGz/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --tag PL /tmp/KPuGusJkGz/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --tag PL /tmp/KPuGusJkGz/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --tag PL 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --vcf-ids /tmp/KPuGusJkGz/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --vcf-ids /tmp/KPuGusJkGz/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom /tmp/KPuGusJkGz/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom /tmp/KPuGusJkGz/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom --vcf-ids /tmp/KPuGusJkGz/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom --vcf-ids /tmp/KPuGusJkGz/check.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/check.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h -,.,. /tmp/KPuGusJkGz/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h -,.,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h .,-,. /tmp/KPuGusJkGz/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h .,-,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert -h .,.,- /tmp/KPuGusJkGz/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert -h .,.,- 2>/dev/null
+.. ok
+
+test_vcf_convert_hls2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -H /<<PKGBUILDDIR>>/test/convert.hls.gt.hap,/<<PKGBUILDDIR>>/test/convert.hls.gt.legend,/<<PKGBUILDDIR>>/test/convert.hls.gt.samples 2>/dev/null | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert_hls2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -H /<<PKGBUILDDIR>>/test/convert.hls.gt.hap,/<<PKGBUILDDIR>>/test/convert.hls.gt.legend,/<<PKGBUILDDIR>>/test/convert.hls.gt.samples -Ou 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert_hs2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample2vcf /<<PKGBUILDDIR>>/test/convert.hs.gt.hap,/<<PKGBUILDDIR>>/test/convert.hs.gt.samples 2>/dev/null | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert_hs2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample2vcf /<<PKGBUILDDIR>>/test/convert.hs.gt.hap,/<<PKGBUILDDIR>>/test/convert.hs.gt.samples -Ou 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf
+ /<<PKGBUILDDIR>>/test/convert.gt.noHead.vcf.new
+.. failed ...
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample -,. /tmp/KPuGusJkGz/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --hapsample -,. 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools convert --hapsample .,- /tmp/KPuGusJkGz/convert.vcf.gz 2>/dev/null
+.. ok
+
+test_vcf_convert:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/convert.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --hapsample .,- 2>/dev/null
+.. ok
+
+test_vcf_convert_gvcf:
+ /<<PKGBUILDDIR>>/bcftools convert --no-version --gvcf2vcf -f /<<PKGBUILDDIR>>/test/gvcf.fa /tmp/KPuGusJkGz/convert.gvcf.vcf.gz 2>/dev/null
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out.new
+.. failed ...
+
+test_vcf_convert_gvcf:
+ /<<PKGBUILDDIR>>/bcftools view -Ob /tmp/KPuGusJkGz/convert.gvcf.vcf.gz | /<<PKGBUILDDIR>>/bcftools convert --gvcf2vcf -f /<<PKGBUILDDIR>>/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out
+ /<<PKGBUILDDIR>>/test/convert.gvcf.out.new
+.. failed ...
+
+test_vcf_convert_tsv2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /<<PKGBUILDDIR>>/test/23andme.fa --tsv2vcf /<<PKGBUILDDIR>>/test/convert.23andme 2>/dev/null
+.. ok
+
+test_vcf_convert_tsv2vcf:
+ /<<PKGBUILDDIR>>/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /<<PKGBUILDDIR>>/test/23andme.fa --tsv2vcf /<<PKGBUILDDIR>>/test/convert.23andme 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools_
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/KPuGusJkGz/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/KPuGusJkGz/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/KPuGusJkGz/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/KPuGusJkGz/consensus.1.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/KPuGusJkGz/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/KPuGusJkGz/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/KPuGusJkGz/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/KPuGusJkGz/consensus.2.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/KPuGusJkGz/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -I -m /<<PKGBUILDDIR>>/test/consensus.tab 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/KPuGusJkGz/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -I -m /<<PKGBUILDDIR>>/test/consensus.tab -c /tmp/KPuGusJkGz/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/KPuGusJkGz/consensus.3.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/KPuGusJkGz/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus_chain:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/KPuGusJkGz/consensus.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa -H 1 -c /tmp/KPuGusJkGz/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/KPuGusJkGz/consensus.4.chain.new
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/KPuGusJkGz/consensus2.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus2.fa -H 1 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/KPuGusJkGz/consensus2.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus2.fa -H 2 2>/dev/null
+.. ok
+
+test_vcf_consensus:
+ /<<PKGBUILDDIR>>/bcftools consensus /tmp/KPuGusJkGz/empty.vcf.gz -f /<<PKGBUILDDIR>>/test/consensus.fa 2>/dev/null
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -b /tmp/KPuGusJkGz/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/KPuGusJkGz/mpileup.bam.urllist 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -b /tmp/KPuGusJkGz/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/KPuGusJkGz/mpileup.cram.urllist 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out
+ /<<PKGBUILDDIR>>/test/mpileup/mpileup.6.out.new
+.. failed ...
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -r17:100-150 -S ^/<<PKGBUILDDIR>>/test/mplp.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -S /<<PKGBUILDDIR>>/test/mplp.9.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -t17:100-150 -G /<<PKGBUILDDIR>>/test/mplp.10.samples -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.1.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.2.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s HG00102 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -s ^HG99999 -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.bam /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -G /<<PKGBUILDDIR>>/test/mplp.11.rgs -f /<<PKGBUILDDIR>>/test/mpileup/mpileup.ref.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/mpileup.3.cram /<<PKGBUILDDIR>>/test/mpileup/mpileup.4.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.bam 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_mpileup:
+ /<<PKGBUILDDIR>>/bcftools mpileup -a AD -f /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.fa -Ob /<<PKGBUILDDIR>>/test/mpileup/indel-AD.1.cram 2>/dev/null | /<<PKGBUILDDIR>>/bcftools view | grep -v ^##bcftools | grep -v ^##reference
+.. ok
+
+test_csq:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq.fa -g /<<PKGBUILDDIR>>/test/csq.gff3 /<<PKGBUILDDIR>>/test/csq.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq.gff3 ...
+Indexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq.1.out
+ /<<PKGBUILDDIR>>/test/csq.1.out.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff /<<PKGBUILDDIR>>/test/csq/ENST00000218032/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff /<<PKGBUILDDIR>>/test/csq/ENST00000218032/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000218032/ENST00000218032.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.gff /<<PKGBUILDDIR>>/test/csq/ENST00000357367/stop-retained.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000357367/ENST00000357367.gff ...
+Indexed 1 transcripts, 4 exons, 3 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.gff /<<PKGBUILDDIR>>/test/csq/ENST00000519442/synon-splice-region-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000519442/ENST00000519442.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.gff /<<PKGBUILDDIR>>/test/csq/ENST00000390520/deletion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000390520/ENST00000390520.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.gff /<<PKGBUILDDIR>>/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000448695/ENST00000448695.gff ...
+Indexed 1 transcripts, 26 exons, 26 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.gff /<<PKGBUILDDIR>>/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000375992/ENST00000375992.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff /<<PKGBUILDDIR>>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff /<<PKGBUILDDIR>>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000536784/ENST00000536784.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.gff /<<PKGBUILDDIR>>/test/csq/ENST00000593942/last-codon-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000593942/ENST00000593942.gff ...
+Indexed 1 transcripts, 7 exons, 4 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff /<<PKGBUILDDIR>>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff /<<PKGBUILDDIR>>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000295641/ENST00000295641.gff ...
+Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff /<<PKGBUILDDIR>>/test/csq/ENST00000373833/boundary-insertion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff /<<PKGBUILDDIR>>/test/csq/ENST00000373833/boundary-insertion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000373833/ENST00000373833.gff ...
+Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff /<<PKGBUILDDIR>>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff /<<PKGBUILDDIR>>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000294661/ENST00000294661.gff ...
+Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.gff /<<PKGBUILDDIR>>/test/csq/ENST00000256452/intron.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000256452/ENST00000256452.gff ...
+Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.gff /<<PKGBUILDDIR>>/test/csq/ENST00000381157/haploid-diploid.vcf | /<<PKGBUILDDIR>>/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000381157/ENST00000381157.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 0 UTRs
+Calling...
+Warning: Skipping site with non-diploid/non-haploid genotypes at X:31180 C>T
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000381157/haploid-diploid.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000381157/haploid-diploid.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff /<<PKGBUILDDIR>>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff /<<PKGBUILDDIR>>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000378322/ENST00000378322.gff ...
+Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.fa -g /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.gff /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/synon.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENSG00000173376/ENSG00000173376.gff ...
+Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.gff /<<PKGBUILDDIR>>/test/csq/ENST00000413103/long-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000413103/ENST00000413103.gff ...
+Indexed 1 transcripts, 2 exons, 0 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.gff /<<PKGBUILDDIR>>/test/csq/ENST00000409523/long-overlapping-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000409523/ENST00000409523.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame2.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame1.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000341065/frame3.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff /<<PKGBUILDDIR>>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000341065/ENST00000341065.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.gff /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000368801/ENST00000368801.gff ...
+Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000368801/compound-lost.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520868/long-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520868/ENST00000520868.gff ...
+Indexed 1 transcripts, 6 exons, 5 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff /<<PKGBUILDDIR>>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff /<<PKGBUILDDIR>>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000543077/ENST00000543077.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff /<<PKGBUILDDIR>>/test/csq/ENST00000303039/not-a-stop.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff /<<PKGBUILDDIR>>/test/csq/ENST00000303039/not-a-stop.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000303039/ENST00000303039.gff ...
+Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000573314/ENST00000573314.gff ...
+Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l
+ /<<PKGBUILDDIR>>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff /<<PKGBUILDDIR>>/test/csq/ENST00000318249/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff /<<PKGBUILDDIR>>/test/csq/ENST00000318249/start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000318249/ENST00000318249.gff ...
+Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.gff /<<PKGBUILDDIR>>/test/csq/ENST00000545279/splice-region-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000545279/ENST00000545279.gff ...
+Indexed 1 transcripts, 9 exons, 7 CDSs, 4 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.gff /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000301246/ENST00000301246.gff ...
+Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000301246/15bp-insert.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.gff /<<PKGBUILDDIR>>/test/csq/ENST00000420670/start-stop-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000420670/ENST00000420670.gff ...
+Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520795/long-inside-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff /<<PKGBUILDDIR>>/test/csq/ENST00000520795/long-inside-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000520795/ENST00000520795.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/snps.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/snps.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/insert3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff /<<PKGBUILDDIR>>/test/csq/ENST00000423372/insert3.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000423372/ENST00000423372.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.gff /<<PKGBUILDDIR>>/test/csq/ENST00000436063/insert-before-utr.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000436063/ENST00000436063.gff ...
+Indexed 1 transcripts, 7 exons, 7 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.gff /<<PKGBUILDDIR>>/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000528237/ENST00000528237.gff ...
+Indexed 1 transcripts, 7 exons, 6 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff /<<PKGBUILDDIR>>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff /<<PKGBUILDDIR>>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000479739/ENST00000479739.gff ...
+Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ambiguous.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff ...
+Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs
+Calling...
+/bin/bash: line 1: 185731 Done /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ENST00000624631.gff /<<PKGBUILDDIR>>/test/csq/ENST00000624631/ambiguous.vcf
+ 185732 | /<<PKGBUILDDIR>>/test/csq/sort-csq
+ 185733 Segmentation fault | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+
+ Non-zero status 139
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.gff /<<PKGBUILDDIR>>/test/csq/ENST00000557788/long-overlap-del.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000557788/ENST00000557788.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff /<<PKGBUILDDIR>>/test/csq/ENST00000329454/boundary-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff /<<PKGBUILDDIR>>/test/csq/ENST00000329454/boundary-deletion.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000329454/ENST00000329454.gff ...
+Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.gff /<<PKGBUILDDIR>>/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000382647/ENST00000382647.gff ...
+Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff /<<PKGBUILDDIR>>/test/csq/ENST00000542803/splice-region.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -l -f /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff /<<PKGBUILDDIR>>/test/csq/ENST00000542803/splice-region.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000542803/ENST00000542803.gff ...
+Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs
+Calling...
+.. ok
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.gff /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000410009/ENST00000410009.gff ...
+Indexed 1 transcripts, 6 exons, 6 CDSs, 2 UTRs
+Calling...
+[W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String
+
+ The outputs differ:
+ /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.txt
+ /<<PKGBUILDDIR>>/test/csq/ENST00000410009/frameshift.txt.new
+.. failed ...
+
+test_csq_real:
+ /<<PKGBUILDDIR>>/bcftools csq -f /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.fa -g /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.gff /<<PKGBUILDDIR>>/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /<<PKGBUILDDIR>>/test/csq/sort-csq | /<<PKGBUILDDIR>>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
+Parsing /<<PKGBUILDDIR>>/test/csq/ENST00000227471/ENST00000227471.gff ...
+Indexed 1 transcripts, 12 exons, 12 CDSs, 2 UTRs
+Calling...
+.. ok
+
+
+Number of tests:
+ total .. 727
+ passed .. 606
+ failed .. 121
+
+Makefile:246: recipe for target 'test-plugins' failed
+make[1]: *** [test-plugins] Error 1
+make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+dh_auto_test: make -j32 test VERBOSE=1 returned exit code 2
+debian/rules:7: recipe for target 'build-arch' failed
+make: *** [build-arch] Error 2
+dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
+--------------------------------------------------------------------------------
+Build finished at 2017-12-11T16:51:35Z
+
+Finished
+--------
+
+
++------------------------------------------------------------------------------+
+| Cleanup |
++------------------------------------------------------------------------------+
+
+Purging /<<BUILDDIR>>
+Not cleaning session: cloned chroot in use
+E: Build failure (dpkg-buildpackage died)
+
++------------------------------------------------------------------------------+
+| Summary |
++------------------------------------------------------------------------------+
+
+Build Architecture: sparc64
+Build Type: any
+Build-Space: 29116
+Build-Time: 136
+Distribution: experimental
+Fail-Stage: build
+Host Architecture: sparc64
+Install-Time: 144
+Job: bcftools_1.6-1
+Machine Architecture: sparc64
+Package: bcftools
+Package-Time: 317
+Source-Version: 1.6-1
+Space: 29116
+Status: attempted
+Version: 1.6-1
+--------------------------------------------------------------------------------
+Finished at 2017-12-11T16:51:35Z
+Build needed 00:05:17, 29116k disk space
diff --git a/get_logs b/get_logs
new file mode 100755
index 0000000..00c1cdf
--- /dev/null
+++ b/get_logs
@@ -0,0 +1,8 @@
+#!/bin/sh
+wget -q -N https://buildd.debian.org/status/fetch.php?pkg=bcftools\&arch=i386\&ver=1.6-1\&stamp=1513008956\&raw=1 -O bcftools_1.6-1_i386.log
+wget -q -N https://buildd.debian.org/status/fetch.php?pkg=bcftools\&arch=mips\&ver=1.6-1\&stamp=1513022280\&raw=1 -O bcftools_1.6-1_mips.log
+wget -q -N https://buildd.debian.org/status/fetch.php?pkg=bcftools\&arch=s390x\&ver=1.6-1\&stamp=1513008500\&raw=1 -O bcftools_1.6-1_s390x.log
+wget -q -N https://buildd.debian.org/status/fetch.php?pkg=bcftools\&arch=kfreebsd-i386\&ver=1.6-1\&stamp=1513009463\&raw=1 -O bcftools_1.6-1_kfreebsd-i386.log
+wget -q -N https://buildd.debian.org/status/fetch.php?pkg=bcftools\&arch=alpha\&ver=1.6-1\&stamp=1513048370\&raw=1 -O bcftools_1.6-1_alpha.log
+wget -q -N https://buildd.debian.org/status/fetch.php?pkg=bcftools\&arch=ppc64\&ver=1.6-1\&stamp=1513010605\&raw=1 -O bcftools_1.6-1_ppc64.log
+wget -q -N https://buildd.debian.org/status/fetch.php?pkg=bcftools\&arch=sparc64\&ver=1.6-1\&stamp=1513011104\&raw=1 -O bcftools_1.6-1_sparc64.log
\ No newline at end of file
--
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