htslib →
1.7-2 →
armhf → 2018-02-19 04:45:17
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| htslib 1.7-2 (armhf) Mon, 19 Feb 2018 04:38:15 +0000 |
+==============================================================================+
Package: htslib
Version: 1.7-2
Source Version: 1.7-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-d42ba723-6ee4-403c-a268-68c280605662' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.6 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.3 MB]
Fetched 22.9 MB in 8s (2729 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...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'htslib' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/htslib.git -b debian/unstable
Please use:
git clone https://anonscm.debian.org/git/debian-med/htslib.git -b debian/unstable
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1194 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main htslib 1.7-2 (dsc) [2339 B]
Get:2 http://172.17.0.1/private buster-staging/main htslib 1.7-2 (tar) [1178 kB]
Get:3 http://172.17.0.1/private buster-staging/main htslib 1.7-2 (diff) [13.8 kB]
Fetched 1194 kB in 0s (5491 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/htslib-eyn0YM/htslib-1.7' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/htslib-eyn0YM' 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-oqDUGy/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.
gpg: keybox '/<<BUILDDIR>>/resolver-oqDUGy/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-oqDUGy/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-oqDUGy/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-oqDUGy/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-oqDUGy/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-oqDUGy/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-oqDUGy/apt_archive ./ Packages [434 B]
Fetched 2110 B in 0s (10.8 kB/s)
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W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 63 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-oqDUGy/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15333 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev
Filtered Build-Depends: debhelper (>= 10), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-htslib-dummy' in '/<<BUILDDIR>>/resolver-oqDUGy/apt_archive/sbuild-build-depends-htslib-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-htslib-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-oqDUGy/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-oqDUGy/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-oqDUGy/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-oqDUGy/apt_archive ./ Sources [529 B]
Get:5 copy:/<<BUILDDIR>>/resolver-oqDUGy/apt_archive ./ Packages [612 B]
Fetched 2474 B in 0s (11.9 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install htslib build dependencies (apt-based resolver)
------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates e2fsprogs-l10n libsasl2-modules openssl
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
libcurl3-gnutls libcurl4-gnutls-dev libfile-stripnondeterminism-perl
libgdbm5 libglib2.0-0 libgssapi-krb5-2 libicu57 libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl-dev
libtimedate-perl libtool libxml2 m4 man-db po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev pkg-config gdbm-l10n krb5-doc krb5-user
liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales publicsuffix libssl-doc
libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
libcurl3-gnutls libcurl4-gnutls-dev libfile-stripnondeterminism-perl
libgdbm5 libglib2.0-0 libgssapi-krb5-2 libicu57 libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl-dev
libtimedate-perl libtool libxml2 m4 man-db po-debconf
sbuild-build-depends-htslib-dummy zlib1g-dev
0 upgraded, 47 newly installed, 0 to remove and 63 not upgraded.
Need to get 21.9 MB/22.3 MB of archives.
After this operation, 73.9 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-oqDUGy/apt_archive ./ sbuild-build-depends-htslib-dummy 0.invalid.0 [896 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.7-1 [96.8 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libgdbm5 armhf 1.14.1-3 [54.0 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.1-1+b1 [1143 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9.2 [12.1 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-1 [32.2 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20171216.1 [75.9 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 16 [16.3 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.3-2 [2651 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
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Get:25 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-2 [132 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.1.4 [1005 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-8.1 [26.9 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.16-2 [59.0 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.16-2 [116 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.16-2 [265 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.16-2 [135 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.30.0-1 [70.6 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.19.1-4 [43.2 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.58.0-2 [275 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libcurl4-gnutls-dev armhf 7.58.0-2 [346 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.2-1.3 [284 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.0g-2 [1371 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23 [24.9 kB]
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Preparing to unpack .../44-zlib1g-dev_1%3a1.2.8.dfsg-5_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Selecting previously unselected package dh-exec.
Preparing to unpack .../45-dh-exec_0.23_armhf.deb ...
Unpacking dh-exec (0.23) ...
Selecting previously unselected package sbuild-build-depends-htslib-dummy.
Preparing to unpack .../46-sbuild-build-depends-htslib-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Setting up libbz2-dev:armhf (1.0.6-8.1) ...
Setting up libarchive-zip-perl (1.60-1) ...
Setting up libnghttp2-14:armhf (1.30.0-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.12-1) ...
Setting up libpsl5:armhf (0.19.1-4) ...
Setting up libssl-dev:armhf (1.1.0g-2) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.54.3-2) ...
No schema files found: doing nothing.
Setting up gettext-base (0.19.8.1-4) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libgdbm5:armhf (1.14.1-3) ...
Setting up libicu57:armhf (57.1-8) ...
Setting up libbsd0:armhf (0.8.7-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-6.1) ...
Setting up libmagic-mgc (1:5.32-1) ...
Setting up libmagic1:armhf (1:5.32-1) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up libssh2-1:armhf (1.8.0-1) ...
Processing triggers for libc-bin (2.26-4+rpi1) ...
Setting up autotools-dev (20171216.1) ...
Setting up liblzma-dev:armhf (5.2.2-1.3) ...
Setting up libkeyutils1:armhf (1.5.9-9.2) ...
Setting up bsdmainutils (11.1.2) ...
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 autopoint (0.19.8.1-4) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.040-1) ...
Setting up gettext (0.19.8.1-4) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-1) ...
Setting up libkrb5support0:armhf (1.16-2) ...
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 (2.8.1-1+b1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up libcurl3-gnutls:armhf (7.58.0-2) ...
Setting up libcurl4-gnutls-dev:armhf (7.58.0-2) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up debhelper (11.1.4) ...
Setting up dh-autoreconf (16) ...
Setting up dh-exec (0.23) ...
Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.26-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.29.1-13+rpi1 dpkg-dev_1.19.0.5 g++-7_7.2.0-19+b1 gcc-7_7.2.0-19+b1 libc6-dev_2.26-4+rpi1 libstdc++-7-dev_7.2.0-19+b1 libstdc++6_7.2.0-19+b1 linux-libc-dev_4.9.51-1+rpi3+b1
Package versions: adduser_3.116 apt_1.6~alpha6 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20171216.1 base-files_10.1+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-13+rpi1 binutils-arm-linux-gnueabihf_2.29.1-13+rpi1 binutils-common_2.29.1-13+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.30.2-0.3 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-19+b1 dash_0.5.8-2.10 debconf_1.5.65 debhelper_11.1.4 debianutils_4.8.4 dh-autoreconf_16 dh-exec_0.23 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.4-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.43.8-2 e2fsprogs_1.43.8-2 e2fsprogs-l10n_1.43.8-2 fakeroot_1.22-2 fdisk_2.30.2-0.3 file_1:5.32-1 findutils_4.6.0+git+20170828-2 g++_4:7.2.0-1d1 g++-7_7.2.0-19+b1 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.2.0-19+b1 gcc-7-base_7.2.0-19+b1 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.4-1 gnupg-agent_2.2.4-1 gnupg-l10n_2.2.4-1 gnupg-utils_2.2.4-1 gpg_2.2.4-1 gpg-agent_2.2.4-1 gpg-wks-client_2.2.4-1 gpg-wks-server_2.2.4-1 gpgconf_2.2.4-1 gpgsm_2.2.4-1 gpgv_2.2.4-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-2 libapt-pkg5.0_1.6~alpha6 libarchive-zip-perl_1.60-1 libasan4_7.2.0-19+b1 libassuan0_2.5.1-1 libatomic1_7.2.0-19+b1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.29.1-13+rpi1 libblkid1_2.30.2-0.3 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.26-4+rpi1 libc-dev-bin_2.26-4+rpi1 libc6_2.26-4+rpi1 libc6-dev_2.26-4+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_7.2.0-19+b1 libcilkrts5_7.2.0-19+b1 libcomerr2_1.43.8-2 libcroco3_0.6.12-2 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.58.0-2 libcurl4-gnutls-dev_7.58.0-2 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.2-1 libdebconfclient0_0.239 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.89-1+rpi1 libdrm2_2.4.89-1+rpi1 libfakeroot_1.22-2 libfdisk1_2.30.2-0.3 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-19+b1 libgcc1_1:7.2.0-19+b1 libgcrypt20_1.8.1-4 libgdbm3_1.8.3-14 libgdbm5_1.14.1-3 libglib2.0-0_2.54.3-2 libgmp10_2:6.1.2+dfsg-2 libgnutls30_3.5.17-1 libgomp1_7.2.0-19+b1 libgpg-error0_1.27-5 libgssapi-krb5-2_1.16-2 libhogweed4_3.4-1 libicu57_57.1-8 libidn11_1.33-2.1 libidn2-0_2.0.4-1.1 libip4tc0_1.6.1-2+b1 libisl15_0.18-1 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.2-0.3 libmpc3_1.1.0-1 libmpfr6_4.0.0-7 libncurses5_6.0+20171125-1 libncursesw5_6.0+20171125-1 libnettle6_3.4-1 libnghttp2-14_1.30.0-1 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-8 libperl5.24_5.24.1-7 libperl5.26_5.26.1-4 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libpsl5_0.19.1-4 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-1 libsmartcols1_2.30.2-0.3 libsqlite3-0_3.22.0-1 libss2_1.43.8-2 libssh2-1_1.8.0-1 libssl-dev_1.1.0g-2 libssl1.1_1.1.0g-2 libstdc++-7-dev_7.2.0-19+b1 libstdc++6_7.2.0-19+b1 libsystemd0_236-2 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20171125-1 libtool_2.4.6-2 libubsan0_7.2.0-19+b1 libudev1_236-2 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.30.2-0.3 libxml2_2.9.4+dfsg1-6.1 linux-base_4.5 linux-libc-dev_4.9.51-1+rpi3+b1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.1-1+b1 mawk_1.3.3-17 mount_2.30.2-0.3 multiarch-support_2.26-4+rpi1 nano_2.9.2-1 ncurses-base_6.0+20171125-1 ncurses-bin_6.0+20171125-1 openssl_1.1.0g-2 passwd_1:4.5-1 patch_2.7.5-1 perl_5.26.1-4 perl-base_5.26.1-4 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-4 pinentry-curses_1.0.0-3 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.11 systemd_236-2 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018c-1 udev_236-2 util-linux_2.30.2-0.3 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Feb 14 12:17:22 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./htslib_1.7-2.dsc
dpkg-source: info: extracting htslib in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking htslib_1.7.orig.tar.gz
dpkg-source: info: unpacking htslib_1.7-2.debian.tar.xz
dpkg-source: info: applying define_PATH_MAX.patch
dpkg-source: info: applying htslib-add-cram_to_bam.patch
dpkg-source: info: applying fPIC.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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-d42ba723-6ee4-403c-a268-68c280605662
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package htslib
dpkg-buildpackage: info: source version 1.7-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build htslib-1.7
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from htslib-1.7/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 distclean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.tmp test/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL*
rm -f libhts.so libhts.so.*
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
rm -f libhts.a bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/sam test/test_bgzf test/test-regidx test/test_view test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/test-bcf-translate test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6
rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk
rm -rf autom4te.cache
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/libhts2.substvars debian/libhts-dev.substvars debian/libhts-private-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files
rm -fr -- debian/libhts2/ debian/tmp/ debian/libhts-dev/ debian/libhts-private-dev/ debian/htslib-test/ debian/tabix/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p
" > debian/autoreconf.before
autoreconf -f -i
find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p
" > debian/autoreconf.after
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# create clean copy of test dir
cp -a test test_backup
autoconf
dh_auto_configure -- --enable-libcurl
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
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 ranlib... ranlib
checking for grep that handles long lines and -e... /bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking how to run the C preprocessor... gcc -E
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/libhts-dev.debhelper.log debian/libhts2.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
# re-try later LDLIBS=-lhts \
PACKAGE_VERSION="1.7-2" \
libdir=/usr/lib/arm-linux-gnueabihf
make -j4 "CFLAGS=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -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. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_libcurl.o hfile_libcurl.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_gcs.o hfile_gcs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_s3.o hfile_s3.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o knetfile.pico knetfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_net.pico hfile_net.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/files.pico cram/files.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -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. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
gcc -shared -Wl,-soname,libhts.so.2 -Wl,-z,relro -Wl,-z,now -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm -lcurl -lcrypto
ln -sf libhts.so libhts.so.2
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o
ranlib libhts.a
gcc -Wl,-z,relro -Wl,-z,now -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 test VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
test/hts_endian
test/fieldarith test/fieldarith.sam
test/hfile
test/test_bgzf test/bgziptest.txt
cd test/tabix && ./test-tabix.sh tabix.tst
Testing tabix...
PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz
PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151
PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812
PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz
PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151
PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812
PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero)
PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz
PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647
PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz
PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200
PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz
PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190
Expected passes: 13
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
REF_PATH=: test/sam test/ce.fa test/faidx.fa
test/test-regidx
cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-}
test_view testing auxf#values.sam, ref auxf.fa:
./test_view -S -b auxf#values.sam > auxf#values.tmp.bam
./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
./test_view -t auxf.fa -S -C auxf#values.sam > auxf#values.tmp.cram
./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -t auxf.fa -C auxf#values.tmp.bam > auxf#values.tmp.bam.cram
./test_view -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
./test_view -t auxf.fa -S -C -o VERSION=3.0 auxf#values.sam > auxf#values.tmp.cram
./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
./test_view -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
./test_view -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
./test_view auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_
./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_
.. ok
test_view testing c1#bounds.sam, ref c1.fa:
./test_view -S -b c1#bounds.sam > c1#bounds.tmp.bam
./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_
./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_
./test_view -t c1.fa -S -C c1#bounds.sam > c1#bounds.tmp.cram
./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
./test_view -t c1.fa -C c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
./test_view -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 c1#bounds.sam > c1#bounds.tmp.cram
./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
./test_view -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
./test_view c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
.. ok
test_view testing c1#clip.sam, ref c1.fa:
./test_view -S -b c1#clip.sam > c1#clip.tmp.bam
./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_
./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_
./test_view -t c1.fa -S -C c1#clip.sam > c1#clip.tmp.cram
./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
./test_view -t c1.fa -C c1#clip.tmp.bam > c1#clip.tmp.bam.cram
./test_view -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 c1#clip.sam > c1#clip.tmp.cram
./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
./test_view -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
./test_view c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
.. ok
test_view testing c1#noseq.sam, ref c1.fa:
./test_view -S -b c1#noseq.sam > c1#noseq.tmp.bam
./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_
./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_
./test_view -t c1.fa -S -C c1#noseq.sam > c1#noseq.tmp.cram
./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
./test_view -t c1.fa -C c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
./test_view -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 c1#noseq.sam > c1#noseq.tmp.cram
./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
./test_view -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
./test_view c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
.. ok
test_view testing c1#pad1.sam, ref c1.fa:
./test_view -S -b c1#pad1.sam > c1#pad1.tmp.bam
./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_
./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_
./test_view -t c1.fa -S -C c1#pad1.sam > c1#pad1.tmp.cram
./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
./test_view -t c1.fa -C c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
./test_view -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 c1#pad1.sam > c1#pad1.tmp.cram
./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
./test_view -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
./test_view c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
.. ok
test_view testing c1#pad2.sam, ref c1.fa:
./test_view -S -b c1#pad2.sam > c1#pad2.tmp.bam
./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_
./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_
./test_view -t c1.fa -S -C c1#pad2.sam > c1#pad2.tmp.cram
./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
./test_view -t c1.fa -C c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
./test_view -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 c1#pad2.sam > c1#pad2.tmp.cram
./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
./test_view -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
./test_view c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
.. ok
test_view testing c1#pad3.sam, ref c1.fa:
./test_view -S -b c1#pad3.sam > c1#pad3.tmp.bam
./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_
./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_
./test_view -t c1.fa -S -C c1#pad3.sam > c1#pad3.tmp.cram
./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -t c1.fa -C c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
./test_view -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 c1#pad3.sam > c1#pad3.tmp.cram
./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
./test_view -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
./test_view c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
.. ok
test_view testing c1#unknown.sam, ref c1.fa:
./test_view -S -b c1#unknown.sam > c1#unknown.tmp.bam
./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_
./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_
./test_view -t c1.fa -S -C c1#unknown.sam > c1#unknown.tmp.cram
./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
./test_view -t c1.fa -C c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
./test_view -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 c1#unknown.sam > c1#unknown.tmp.cram
./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
./test_view -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
./test_view c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
.. ok
test_view testing c2#pad.sam, ref c2.fa:
./test_view -S -b c2#pad.sam > c2#pad.tmp.bam
./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_
./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_
./test_view -t c2.fa -S -C c2#pad.sam > c2#pad.tmp.cram
./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
./test_view -t c2.fa -C c2#pad.tmp.bam > c2#pad.tmp.bam.cram
./test_view -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
./test_view -t c2.fa -S -C -o VERSION=3.0 c2#pad.sam > c2#pad.tmp.cram
./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
./test_view -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
./test_view -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
./test_view c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
.. ok
test_view testing ce#1.sam, ref ce.fa:
./test_view -S -b ce#1.sam > ce#1.tmp.bam
./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_
./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#1.sam > ce#1.tmp.cram
./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
./test_view -t ce.fa -C ce#1.tmp.bam > ce#1.tmp.bam.cram
./test_view -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 ce#1.sam > ce#1.tmp.cram
./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
./test_view -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram
./test_view ce#1.tmp.cram > ce#1.tmp.cram.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
.. ok
test_view testing ce#2.sam, ref ce.fa:
./test_view -S -b ce#2.sam > ce#2.tmp.bam
./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_
./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#2.sam > ce#2.tmp.cram
./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
./test_view -t ce.fa -C ce#2.tmp.bam > ce#2.tmp.bam.cram
./test_view -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 ce#2.sam > ce#2.tmp.cram
./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
./test_view -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram
./test_view ce#2.tmp.cram > ce#2.tmp.cram.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
.. ok
test_view testing ce#5.sam, ref ce.fa:
./test_view -S -b ce#5.sam > ce#5.tmp.bam
./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_
./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#5.sam > ce#5.tmp.cram
./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -t ce.fa -C ce#5.tmp.bam > ce#5.tmp.bam.cram
./test_view -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 ce#5.sam > ce#5.tmp.cram
./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
./test_view -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram
./test_view ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
.. ok
test_view testing ce#5b.sam, ref ce.fa:
./test_view -S -b ce#5b.sam > ce#5b.tmp.bam
./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_
./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#5b.sam > ce#5b.tmp.cram
./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
./test_view -t ce.fa -C ce#5b.tmp.bam > ce#5b.tmp.bam.cram
./test_view -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 ce#5b.sam > ce#5b.tmp.cram
./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
./test_view -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
./test_view ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_
./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_
.. ok
test_view testing ce#large_seq.sam, ref ce.fa:
./test_view -S -b ce#large_seq.sam > ce#large_seq.tmp.bam
./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_
./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#large_seq.sam > ce#large_seq.tmp.cram
./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -t ce.fa -C ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
./test_view -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
./test_view ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 ce#large_seq.sam > ce#large_seq.tmp.cram
./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
./test_view -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
./test_view ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
./test_view ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
.. ok
test_view testing ce#supp.sam, ref ce.fa:
./test_view -S -b ce#supp.sam > ce#supp.tmp.bam
./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_
./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#supp.sam > ce#supp.tmp.cram
./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -t ce.fa -C ce#supp.tmp.bam > ce#supp.tmp.bam.cram
./test_view -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 ce#supp.sam > ce#supp.tmp.cram
./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
./test_view -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
./test_view ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
.. ok
test_view testing ce#tag_depadded.sam, ref ce.fa:
./test_view -S -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_
./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
./test_view -t ce.fa -C ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
./test_view -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
./test_view -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
./test_view ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
.. ok
test_view testing ce#tag_padded.sam, ref ce.fa:
./test_view -S -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_
./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#tag_padded.sam > ce#tag_padded.tmp.cram
./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
./test_view -t ce.fa -C ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
./test_view -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 ce#tag_padded.sam > ce#tag_padded.tmp.cram
./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
./test_view -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
./test_view ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
.. ok
test_view testing ce#unmap.sam, ref ce.fa:
./test_view -S -b ce#unmap.sam > ce#unmap.tmp.bam
./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_
./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#unmap.sam > ce#unmap.tmp.cram
./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
./test_view -t ce.fa -C ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
./test_view -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 ce#unmap.sam > ce#unmap.tmp.cram
./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
./test_view -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
./test_view ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
.. ok
test_view testing ce#unmap1.sam, ref ce.fa:
./test_view -S -b ce#unmap1.sam > ce#unmap1.tmp.bam
./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_
./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#unmap1.sam > ce#unmap1.tmp.cram
./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
./test_view -t ce.fa -C ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
./test_view -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 ce#unmap1.sam > ce#unmap1.tmp.cram
./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
./test_view -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
./test_view ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
.. ok
test_view testing ce#unmap2.sam, ref ce.fa:
./test_view -S -b ce#unmap2.sam > ce#unmap2.tmp.bam
./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_
./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_
./test_view -t ce.fa -S -C ce#unmap2.sam > ce#unmap2.tmp.cram
./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
./test_view -t ce.fa -C ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
./test_view -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 ce#unmap2.sam > ce#unmap2.tmp.cram
./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
./test_view -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
./test_view ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
.. ok
test_view testing md#1.sam, ref md.fa:
./test_view -S -b md#1.sam > md#1.tmp.bam
./test_view md#1.tmp.bam > md#1.tmp.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.sam_
./test_view -t md.fa -S -C md#1.sam > md#1.tmp.cram
./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_
./compare_sam.pl md#1.sam md#1.tmp.cram.sam_
./test_view -t md.fa -C md#1.tmp.bam > md#1.tmp.bam.cram
./test_view -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam
./test_view md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_
./test_view -t md.fa -S -C -o VERSION=3.0 md#1.sam > md#1.tmp.cram
./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_
./compare_sam.pl md#1.sam md#1.tmp.cram.sam_
./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram
./test_view -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam
./test_view md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_
./test_view -t md.fa -C -o VERSION=2.1 md#1.tmp.cram > md#1.tmp.cram.cram
./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.cram.cram > md#1.tmp.cram
./test_view md#1.tmp.cram > md#1.tmp.cram.sam_
./compare_sam.pl md#1.sam md#1.tmp.cram.sam_
.. ok
test_view testing xx#blank.sam, ref xx.fa:
./test_view -S -b xx#blank.sam > xx#blank.tmp.bam
./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_
./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#blank.sam > xx#blank.tmp.cram
./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -t xx.fa -C xx#blank.tmp.bam > xx#blank.tmp.bam.cram
./test_view -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 xx#blank.sam > xx#blank.tmp.cram
./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
./test_view -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
./test_view xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
.. ok
test_view testing xx#large_aux.sam, ref xx.fa:
./test_view -S -b xx#large_aux.sam > xx#large_aux.tmp.bam
./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_
./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#large_aux.sam > xx#large_aux.tmp.cram
./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -t xx.fa -C xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
./test_view -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
./test_view xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 xx#large_aux.sam > xx#large_aux.tmp.cram
./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
./test_view -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
./test_view xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
./test_view xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20
./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_
.. ok
test_view testing xx#large_aux2.sam, ref xx.fa:
./test_view -S -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_
./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#large_aux2.sam > xx#large_aux2.tmp.cram
./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
./test_view -t xx.fa -C xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
./test_view -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 xx#large_aux2.sam > xx#large_aux2.tmp.cram
./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
./test_view -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
./test_view xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
.. ok
test_view testing xx#minimal.sam, ref xx.fa:
./test_view -S -b xx#minimal.sam > xx#minimal.tmp.bam
./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_
./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#minimal.sam > xx#minimal.tmp.cram
./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
./test_view -t xx.fa -C xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
./test_view -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 xx#minimal.sam > xx#minimal.tmp.cram
./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
./test_view -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
./test_view xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
.. ok
test_view testing xx#pair.sam, ref xx.fa:
./test_view -S -b xx#pair.sam > xx#pair.tmp.bam
./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_
./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#pair.sam > xx#pair.tmp.cram
./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -t xx.fa -C xx#pair.tmp.bam > xx#pair.tmp.bam.cram
./test_view -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 xx#pair.sam > xx#pair.tmp.cram
./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
./test_view -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
./test_view xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
.. ok
test_view testing xx#repeated.sam, ref xx.fa:
./test_view -S -b xx#repeated.sam > xx#repeated.tmp.bam
./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_
./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#repeated.sam > xx#repeated.tmp.cram
./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
./test_view -t xx.fa -C xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
./test_view -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 xx#repeated.sam > xx#repeated.tmp.cram
./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
./test_view -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
./test_view xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
.. ok
test_view testing xx#rg.sam, ref xx.fa:
./test_view -S -b xx#rg.sam > xx#rg.tmp.bam
./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_
./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#rg.sam > xx#rg.tmp.cram
./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
./test_view -t xx.fa -C xx#rg.tmp.bam > xx#rg.tmp.bam.cram
./test_view -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 xx#rg.sam > xx#rg.tmp.cram
./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
./test_view -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
./test_view xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
.. ok
test_view testing xx#tlen.sam, ref xx.fa:
./test_view -S -b xx#tlen.sam > xx#tlen.tmp.bam
./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_
./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#tlen.sam > xx#tlen.tmp.cram
./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -t xx.fa -C xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
./test_view -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 xx#tlen.sam > xx#tlen.tmp.cram
./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
./test_view -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
./test_view xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
.. ok
test_view testing xx#tlen2.sam, ref xx.fa:
./test_view -S -b xx#tlen2.sam > xx#tlen2.tmp.bam
./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_
./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#tlen2.sam > xx#tlen2.tmp.cram
./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
./test_view -t xx.fa -C xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
./test_view -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 xx#tlen2.sam > xx#tlen2.tmp.cram
./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
./test_view -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
./test_view xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
.. ok
test_view testing xx#triplet.sam, ref xx.fa:
./test_view -S -b xx#triplet.sam > xx#triplet.tmp.bam
./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_
./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#triplet.sam > xx#triplet.tmp.cram
./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
./test_view -t xx.fa -C xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
./test_view -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 xx#triplet.sam > xx#triplet.tmp.cram
./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
./test_view -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
./test_view xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
.. ok
test_view testing xx#unsorted.sam, ref xx.fa:
./test_view -S -b xx#unsorted.sam > xx#unsorted.tmp.bam
./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_
./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_
./test_view -t xx.fa -S -C xx#unsorted.sam > xx#unsorted.tmp.cram
./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
./test_view -t xx.fa -C xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 xx#unsorted.sam > xx#unsorted.tmp.cram
./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
./test_view xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
.. ok
test_view testing auxf#values.sam, ref auxf.fa:
./test_view -@4 -S -b auxf#values.sam > auxf#values.tmp.bam
./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
./test_view -@4 -t auxf.fa -S -C auxf#values.sam > auxf#values.tmp.cram
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -C auxf#values.tmp.bam > auxf#values.tmp.bam.cram
./test_view -@4 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
./test_view -@4 auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
./test_view -@4 -t auxf.fa -S -C -o VERSION=3.0 auxf#values.sam > auxf#values.tmp.cram
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
./test_view -@4 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
./test_view -@4 auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
./test_view -@4 -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
./test_view -@4 auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_
./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_
.. ok
test_view testing c1#bounds.sam, ref c1.fa:
./test_view -@4 -S -b c1#bounds.sam > c1#bounds.tmp.bam
./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_
./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C c1#bounds.sam > c1#bounds.tmp.cram
./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
./test_view -@4 -t c1.fa -C c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
./test_view -@4 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
./test_view -@4 c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=3.0 c1#bounds.sam > c1#bounds.tmp.cram
./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
./test_view -@4 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
./test_view -@4 c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
./test_view -@4 c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
.. ok
test_view testing c1#clip.sam, ref c1.fa:
./test_view -@4 -S -b c1#clip.sam > c1#clip.tmp.bam
./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_
./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C c1#clip.sam > c1#clip.tmp.cram
./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
./test_view -@4 -t c1.fa -C c1#clip.tmp.bam > c1#clip.tmp.bam.cram
./test_view -@4 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
./test_view -@4 c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=3.0 c1#clip.sam > c1#clip.tmp.cram
./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
./test_view -@4 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
./test_view -@4 c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
./test_view -@4 c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
.. ok
test_view testing c1#noseq.sam, ref c1.fa:
./test_view -@4 -S -b c1#noseq.sam > c1#noseq.tmp.bam
./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_
./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C c1#noseq.sam > c1#noseq.tmp.cram
./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
./test_view -@4 -t c1.fa -C c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
./test_view -@4 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
./test_view -@4 c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=3.0 c1#noseq.sam > c1#noseq.tmp.cram
./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
./test_view -@4 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
./test_view -@4 c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
./test_view -@4 c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
.. ok
test_view testing c1#pad1.sam, ref c1.fa:
./test_view -@4 -S -b c1#pad1.sam > c1#pad1.tmp.bam
./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_
./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C c1#pad1.sam > c1#pad1.tmp.cram
./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
./test_view -@4 -t c1.fa -C c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
./test_view -@4 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
./test_view -@4 c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=3.0 c1#pad1.sam > c1#pad1.tmp.cram
./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
./test_view -@4 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
./test_view -@4 c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
./test_view -@4 c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
.. ok
test_view testing c1#pad2.sam, ref c1.fa:
./test_view -@4 -S -b c1#pad2.sam > c1#pad2.tmp.bam
./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_
./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C c1#pad2.sam > c1#pad2.tmp.cram
./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
./test_view -@4 -t c1.fa -C c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
./test_view -@4 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
./test_view -@4 c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=3.0 c1#pad2.sam > c1#pad2.tmp.cram
./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
./test_view -@4 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
./test_view -@4 c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
./test_view -@4 c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
.. ok
test_view testing c1#pad3.sam, ref c1.fa:
./test_view -@4 -S -b c1#pad3.sam > c1#pad3.tmp.bam
./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_
./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C c1#pad3.sam > c1#pad3.tmp.cram
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -C c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
./test_view -@4 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
./test_view -@4 c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=3.0 c1#pad3.sam > c1#pad3.tmp.cram
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
./test_view -@4 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
./test_view -@4 c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
./test_view -@4 c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
.. ok
test_view testing c1#unknown.sam, ref c1.fa:
./test_view -@4 -S -b c1#unknown.sam > c1#unknown.tmp.bam
./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_
./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C c1#unknown.sam > c1#unknown.tmp.cram
./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
./test_view -@4 -t c1.fa -C c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
./test_view -@4 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
./test_view -@4 c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=3.0 c1#unknown.sam > c1#unknown.tmp.cram
./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
./test_view -@4 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
./test_view -@4 c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
./test_view -@4 c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
.. ok
test_view testing c2#pad.sam, ref c2.fa:
./test_view -@4 -S -b c2#pad.sam > c2#pad.tmp.bam
./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_
./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_
./test_view -@4 -t c2.fa -S -C c2#pad.sam > c2#pad.tmp.cram
./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
./test_view -@4 -t c2.fa -C c2#pad.tmp.bam > c2#pad.tmp.bam.cram
./test_view -@4 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
./test_view -@4 c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
./test_view -@4 -t c2.fa -S -C -o VERSION=3.0 c2#pad.sam > c2#pad.tmp.cram
./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
./test_view -@4 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
./test_view -@4 c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
./test_view -@4 -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
./test_view -@4 c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
.. ok
test_view testing ce#1.sam, ref ce.fa:
./test_view -@4 -S -b ce#1.sam > ce#1.tmp.bam
./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_
./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C ce#1.sam > ce#1.tmp.cram
./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
./test_view -@4 -t ce.fa -C ce#1.tmp.bam > ce#1.tmp.bam.cram
./test_view -@4 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
./test_view -@4 ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=3.0 ce#1.sam > ce#1.tmp.cram
./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
./test_view -@4 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
./test_view -@4 ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram
./test_view -@4 ce#1.tmp.cram > ce#1.tmp.cram.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
.. ok
test_view testing ce#2.sam, ref ce.fa:
./test_view -@4 -S -b ce#2.sam > ce#2.tmp.bam
./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_
./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C ce#2.sam > ce#2.tmp.cram
./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
./test_view -@4 -t ce.fa -C ce#2.tmp.bam > ce#2.tmp.bam.cram
./test_view -@4 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
./test_view -@4 ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=3.0 ce#2.sam > ce#2.tmp.cram
./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
./test_view -@4 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
./test_view -@4 ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram
./test_view -@4 ce#2.tmp.cram > ce#2.tmp.cram.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
.. ok
test_view testing ce#5.sam, ref ce.fa:
./test_view -@4 -S -b ce#5.sam > ce#5.tmp.bam
./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_
./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C ce#5.sam > ce#5.tmp.cram
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -C ce#5.tmp.bam > ce#5.tmp.bam.cram
./test_view -@4 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
./test_view -@4 ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=3.0 ce#5.sam > ce#5.tmp.cram
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
./test_view -@4 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
./test_view -@4 ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram
./test_view -@4 ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
.. ok
test_view testing ce#5b.sam, ref ce.fa:
./test_view -@4 -S -b ce#5b.sam > ce#5b.tmp.bam
./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_
./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C ce#5b.sam > ce#5b.tmp.cram
./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
./test_view -@4 -t ce.fa -C ce#5b.tmp.bam > ce#5b.tmp.bam.cram
./test_view -@4 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
./test_view -@4 ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=3.0 ce#5b.sam > ce#5b.tmp.cram
./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
./test_view -@4 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
./test_view -@4 ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
./test_view -@4 ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_
./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_
.. ok
test_view testing ce#large_seq.sam, ref ce.fa:
./test_view -@4 -S -b ce#large_seq.sam > ce#large_seq.tmp.bam
./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_
./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C ce#large_seq.sam > ce#large_seq.tmp.cram
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -C ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
./test_view -@4 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
./test_view -@4 ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=3.0 ce#large_seq.sam > ce#large_seq.tmp.cram
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
./test_view -@4 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
./test_view -@4 ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
./test_view -@4 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
.. ok
test_view testing ce#supp.sam, ref ce.fa:
./test_view -@4 -S -b ce#supp.sam > ce#supp.tmp.bam
./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_
./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C ce#supp.sam > ce#supp.tmp.cram
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -C ce#supp.tmp.bam > ce#supp.tmp.bam.cram
./test_view -@4 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
./test_view -@4 ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=3.0 ce#supp.sam > ce#supp.tmp.cram
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
./test_view -@4 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
./test_view -@4 ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
./test_view -@4 ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
.. ok
test_view testing ce#tag_depadded.sam, ref ce.fa:
./test_view -@4 -S -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_
./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
./test_view -@4 -t ce.fa -C ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
./test_view -@4 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
./test_view -@4 ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=3.0 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
./test_view -@4 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
./test_view -@4 ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
./test_view -@4 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
.. ok
test_view testing ce#tag_padded.sam, ref ce.fa:
./test_view -@4 -S -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_
./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C ce#tag_padded.sam > ce#tag_padded.tmp.cram
./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
./test_view -@4 -t ce.fa -C ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
./test_view -@4 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
./test_view -@4 ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=3.0 ce#tag_padded.sam > ce#tag_padded.tmp.cram
./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
./test_view -@4 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
./test_view -@4 ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
./test_view -@4 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
.. ok
test_view testing ce#unmap.sam, ref ce.fa:
./test_view -@4 -S -b ce#unmap.sam > ce#unmap.tmp.bam
./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_
./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C ce#unmap.sam > ce#unmap.tmp.cram
./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
./test_view -@4 -t ce.fa -C ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
./test_view -@4 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
./test_view -@4 ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=3.0 ce#unmap.sam > ce#unmap.tmp.cram
./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
./test_view -@4 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
./test_view -@4 ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
./test_view -@4 ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
.. ok
test_view testing ce#unmap1.sam, ref ce.fa:
./test_view -@4 -S -b ce#unmap1.sam > ce#unmap1.tmp.bam
./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_
./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C ce#unmap1.sam > ce#unmap1.tmp.cram
./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
./test_view -@4 -t ce.fa -C ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
./test_view -@4 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
./test_view -@4 ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=3.0 ce#unmap1.sam > ce#unmap1.tmp.cram
./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
./test_view -@4 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
./test_view -@4 ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
./test_view -@4 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
.. ok
test_view testing ce#unmap2.sam, ref ce.fa:
./test_view -@4 -S -b ce#unmap2.sam > ce#unmap2.tmp.bam
./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_
./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C ce#unmap2.sam > ce#unmap2.tmp.cram
./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
./test_view -@4 -t ce.fa -C ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
./test_view -@4 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
./test_view -@4 ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=3.0 ce#unmap2.sam > ce#unmap2.tmp.cram
./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
./test_view -@4 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
./test_view -@4 ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
./test_view -@4 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
.. ok
test_view testing md#1.sam, ref md.fa:
./test_view -@4 -S -b md#1.sam > md#1.tmp.bam
./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.sam_
./test_view -@4 -t md.fa -S -C md#1.sam > md#1.tmp.cram
./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_
./compare_sam.pl md#1.sam md#1.tmp.cram.sam_
./test_view -@4 -t md.fa -C md#1.tmp.bam > md#1.tmp.bam.cram
./test_view -@4 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam
./test_view -@4 md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_
./test_view -@4 -t md.fa -S -C -o VERSION=3.0 md#1.sam > md#1.tmp.cram
./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_
./compare_sam.pl md#1.sam md#1.tmp.cram.sam_
./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram
./test_view -@4 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam
./test_view -@4 md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_
./test_view -@4 -t md.fa -C -o VERSION=2.1 md#1.tmp.cram > md#1.tmp.cram.cram
./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.cram.cram > md#1.tmp.cram
./test_view -@4 md#1.tmp.cram > md#1.tmp.cram.sam_
./compare_sam.pl md#1.sam md#1.tmp.cram.sam_
.. ok
test_view testing xx#blank.sam, ref xx.fa:
./test_view -@4 -S -b xx#blank.sam > xx#blank.tmp.bam
./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_
./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C xx#blank.sam > xx#blank.tmp.cram
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -C xx#blank.tmp.bam > xx#blank.tmp.bam.cram
./test_view -@4 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
./test_view -@4 xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=3.0 xx#blank.sam > xx#blank.tmp.cram
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
./test_view -@4 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
./test_view -@4 xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
./test_view -@4 xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
.. ok
test_view testing xx#large_aux.sam, ref xx.fa:
./test_view -@4 -S -b xx#large_aux.sam > xx#large_aux.tmp.bam
./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_
./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C xx#large_aux.sam > xx#large_aux.tmp.cram
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -C xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
./test_view -@4 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
./test_view -@4 xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=3.0 xx#large_aux.sam > xx#large_aux.tmp.cram
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
./test_view -@4 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
./test_view -@4 xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
./test_view -@4 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20
./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_
.. ok
test_view testing xx#large_aux2.sam, ref xx.fa:
./test_view -@4 -S -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_
./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C xx#large_aux2.sam > xx#large_aux2.tmp.cram
./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
./test_view -@4 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
./test_view -@4 xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=3.0 xx#large_aux2.sam > xx#large_aux2.tmp.cram
./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
./test_view -@4 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
./test_view -@4 xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
./test_view -@4 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
.. ok
test_view testing xx#minimal.sam, ref xx.fa:
./test_view -@4 -S -b xx#minimal.sam > xx#minimal.tmp.bam
./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_
./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C xx#minimal.sam > xx#minimal.tmp.cram
./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
./test_view -@4 -t xx.fa -C xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
./test_view -@4 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
./test_view -@4 xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=3.0 xx#minimal.sam > xx#minimal.tmp.cram
./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
./test_view -@4 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
./test_view -@4 xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
./test_view -@4 xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
.. ok
test_view testing xx#pair.sam, ref xx.fa:
./test_view -@4 -S -b xx#pair.sam > xx#pair.tmp.bam
./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_
./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C xx#pair.sam > xx#pair.tmp.cram
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -C xx#pair.tmp.bam > xx#pair.tmp.bam.cram
./test_view -@4 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
./test_view -@4 xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=3.0 xx#pair.sam > xx#pair.tmp.cram
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
./test_view -@4 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
./test_view -@4 xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
./test_view -@4 xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
.. ok
test_view testing xx#repeated.sam, ref xx.fa:
./test_view -@4 -S -b xx#repeated.sam > xx#repeated.tmp.bam
./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_
./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C xx#repeated.sam > xx#repeated.tmp.cram
./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
./test_view -@4 -t xx.fa -C xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
./test_view -@4 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
./test_view -@4 xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=3.0 xx#repeated.sam > xx#repeated.tmp.cram
./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
./test_view -@4 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
./test_view -@4 xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
./test_view -@4 xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
.. ok
test_view testing xx#rg.sam, ref xx.fa:
./test_view -@4 -S -b xx#rg.sam > xx#rg.tmp.bam
./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_
./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C xx#rg.sam > xx#rg.tmp.cram
./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
./test_view -@4 -t xx.fa -C xx#rg.tmp.bam > xx#rg.tmp.bam.cram
./test_view -@4 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
./test_view -@4 xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=3.0 xx#rg.sam > xx#rg.tmp.cram
./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
./test_view -@4 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
./test_view -@4 xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
./test_view -@4 xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
.. ok
test_view testing xx#tlen.sam, ref xx.fa:
./test_view -@4 -S -b xx#tlen.sam > xx#tlen.tmp.bam
./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_
./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C xx#tlen.sam > xx#tlen.tmp.cram
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -C xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
./test_view -@4 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
./test_view -@4 xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=3.0 xx#tlen.sam > xx#tlen.tmp.cram
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
./test_view -@4 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
./test_view -@4 xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
./test_view -@4 xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
.. ok
test_view testing xx#tlen2.sam, ref xx.fa:
./test_view -@4 -S -b xx#tlen2.sam > xx#tlen2.tmp.bam
./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_
./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C xx#tlen2.sam > xx#tlen2.tmp.cram
./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
./test_view -@4 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
./test_view -@4 xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=3.0 xx#tlen2.sam > xx#tlen2.tmp.cram
./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
./test_view -@4 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
./test_view -@4 xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
./test_view -@4 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
.. ok
test_view testing xx#triplet.sam, ref xx.fa:
./test_view -@4 -S -b xx#triplet.sam > xx#triplet.tmp.bam
./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_
./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C xx#triplet.sam > xx#triplet.tmp.cram
./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
./test_view -@4 -t xx.fa -C xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
./test_view -@4 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
./test_view -@4 xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=3.0 xx#triplet.sam > xx#triplet.tmp.cram
./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
./test_view -@4 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
./test_view -@4 xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
./test_view -@4 xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
.. ok
test_view testing xx#unsorted.sam, ref xx.fa:
./test_view -@4 -S -b xx#unsorted.sam > xx#unsorted.tmp.bam
./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_
./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C xx#unsorted.sam > xx#unsorted.tmp.cram
./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
./test_view -@4 -t xx.fa -C xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
./test_view -@4 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
./test_view -@4 xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=3.0 xx#unsorted.sam > xx#unsorted.tmp.cram
./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
./test_view -@4 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
./test_view -@4 xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
./test_view -@4 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
.. ok
test_vcf_api:
/<<PKGBUILDDIR>>/test/test-vcf-api /tmp/7tBz_Eq5tW/test-vcf-api.bcf
.. ok
test_vcf_sweep:
/<<PKGBUILDDIR>>/test/test-vcf-sweep /tmp/7tBz_Eq5tW/test-vcf-api.bcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/htsfile -ch /<<PKGBUILDDIR>>/test/test-vcf-hdr-in.vcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/htsfile -c /<<PKGBUILDDIR>>/test/formatcols.vcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/htsfile -c /<<PKGBUILDDIR>>/test/noroundtrip.vcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/htsfile -c /<<PKGBUILDDIR>>/test/formatmissing.vcf
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/7tBz_Eq5tW -s 1408205651
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/7tBz_Eq5tW -s 323357693
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/7tBz_Eq5tW -s 957933405
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/7tBz_Eq5tW -s 912766747
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/7tBz_Eq5tW -s 1518357962
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/7tBz_Eq5tW -s 663417216
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/7tBz_Eq5tW -s 882075139
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/7tBz_Eq5tW -s 681920248
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/7tBz_Eq5tW -s 160775541
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/7tBz_Eq5tW -s 1445005599
.. ok
test_command:
/<<PKGBUILDDIR>>/test/test-bcf-translate -
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/7tBz_Eq5tW/headernul0.bam
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/7tBz_Eq5tW/headernul1.bam
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/7tBz_Eq5tW/headernul678.bam
.. ok
test_rebgzip:
/<<PKGBUILDDIR>>/bgzip -I /<<PKGBUILDDIR>>/test/bgziptest.txt.gz.gzi -c -g /<<PKGBUILDDIR>>/test/bgziptest.txt
.. ok
test-logging:
/<<PKGBUILDDIR>>/test/test-logging.pl
.. ok
Number of tests:
total .. 86
passed .. 86
failed .. 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
rm -f -- debian/libhts2.substvars debian/libhts-dev.substvars debian/tabix.substvars
rm -fr -- debian/.debhelper/generated/libhts2/ debian/libhts2/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/tabix/ debian/tabix/
rm -f debian/libhts-dev.debhelper.log debian/libhts2.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \
rm /<<PKGBUILDDIR>>/test/${binary} ; \
done
dh_auto_install -- \
prefix=/usr \
libdir=/usr/lib/arm-linux-gnueabihf \
PACKAGE_VERSION="1.7-2"
install -d debian/libhts2 debian/libhts-dev debian/tabix
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr libdir=/usr/lib/arm-linux-gnueabihf PACKAGE_VERSION=1.7-2
make[2]: Entering directory '/<<PKGBUILDDIR>>'
echo '#define HTS_VERSION "1.7-2"' > version.h
mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp/usr/bin /<<PKGBUILDDIR>>/debian/tmp/usr/include /<<PKGBUILDDIR>>/debian/tmp/usr/include/htslib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man5 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig
gcc -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c
if test -n ""; then mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp; fi
gcc -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/arm-linux-gnueabihf#g;s#@-PACKAGE_VERSION@#1.7-2#g' htslib.pc.tmp > /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o
ranlib libhts.a
gcc -shared -Wl,-soname,libhts.so.2 -Wl,-z,relro -Wl,-z,now -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
ln -sf libhts.so libhts.so.2
install -p -m 644 libhts.so /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.7-2
ln -sf libhts.so.1.7-2 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so
ln -sf libhts.so.1.7-2 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.2
install -p bgzip htsfile tabix /<<PKGBUILDDIR>>/debian/tmp/usr/bin
if test -n ""; then install -p /<<PKGBUILDDIR>>/debian/tmp; fi
install -p -m 644 htslib/*.h /<<PKGBUILDDIR>>/debian/tmp/usr/include/htslib
install -p -m 644 libhts.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a
install -p -m 644 htsfile.1 tabix.1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man5
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# restore clean copy of test dir before dh_install is run
# This should not be done earlier since dh_auto_install contains some unconditional removals
rm -f -r test
mv test_backup test
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
install -d debian/libhts2/usr/lib/arm-linux-gnueabihf
cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.7-2 debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.2 debian/libhts2/usr/lib/arm-linux-gnueabihf/
install -d debian/.debhelper/generated/libhts2
install -d debian/libhts-dev/usr/include
cp --reflink=auto -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/
install -d debian/libhts-dev/usr/lib/arm-linux-gnueabihf
cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so debian/libhts-dev/usr/lib/arm-linux-gnueabihf/
install -d debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig/
install -d debian/libhts-dev/usr/share/man/man5
cp --reflink=auto -a debian/tmp/usr/share/man/man5/faidx.5 debian/tmp/usr/share/man/man5/sam.5 debian/tmp/usr/share/man/man5/vcf.5 debian/libhts-dev/usr/share/man/man5/
install -d debian/.debhelper/generated/libhts-dev
install -d debian/.debhelper/generated/libhts-private-dev
install -d debian/.debhelper/generated/htslib-test
install -d debian/tabix/usr/bin
cp --reflink=auto -a ./bgzip ./htsfile ./tabix debian/tabix/usr/bin/
install -d debian/.debhelper/generated/tabix
dh_installdocs -a
install -d debian/libhts2/usr/share/doc/libhts2
install -p -m0644 debian/copyright debian/libhts2/usr/share/doc/libhts2/copyright
install -d debian/libhts-dev/usr/share/doc/libhts-dev
cp --reflink=auto -a ./debian/README.test debian/libhts-dev/usr/share/doc/libhts-dev
chown -R 0:0 debian/libhts-dev/usr/share/doc
chmod -R u\+rw,go=rX debian/libhts-dev/usr/share/doc
install -p -m0644 debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright
install -d debian/tabix/usr/share/doc/tabix
install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright
rm -f debian/libhts-dev.debhelper.log debian/libhts2.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs NEWS
install -p -m0644 debian/changelog debian/libhts2/usr/share/doc/libhts2/changelog.Debian
install -p -m0644 NEWS debian/libhts2/usr/share/doc/libhts2/changelog
install -p -m0644 debian/changelog debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian
install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog
install -p -m0644 debian/changelog debian/tabix/usr/share/doc/tabix/changelog.Debian
install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installman -a
install -d debian/tabix/usr/share/man/man1/
install -p -m0644 ./htsfile.1 debian/tabix/usr/share/man/man1/htsfile.1
install -p -m0644 ./tabix.1 debian/tabix/usr/share/man/man1/tabix.1
man -l --recode UTF-8 ./debian/libhts-dev/usr/share/man/man5/faidx.5 > debian/libhts-dev/usr/share/man/man5/faidx.5.dh-new
man -l --recode UTF-8 ./debian/libhts-dev/usr/share/man/man5/sam.5 > debian/libhts-dev/usr/share/man/man5/sam.5.dh-new
man -l --recode UTF-8 ./debian/tabix/usr/share/man/man1/htsfile.1 > debian/tabix/usr/share/man/man1/htsfile.1.dh-new
mv debian/libhts-dev/usr/share/man/man5/sam.5.dh-new debian/libhts-dev/usr/share/man/man5/sam.5
man -l --recode UTF-8 ./debian/tabix/usr/share/man/man1/tabix.1 > debian/tabix/usr/share/man/man1/tabix.1.dh-new
mv debian/libhts-dev/usr/share/man/man5/faidx.5.dh-new debian/libhts-dev/usr/share/man/man5/faidx.5
man -l --recode UTF-8 ./debian/libhts-dev/usr/share/man/man5/vcf.5 > debian/libhts-dev/usr/share/man/man5/vcf.5.dh-new
mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1
chmod 0644 -- debian/tabix/usr/share/man/man1/htsfile.1
mv debian/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1
chmod 0644 -- debian/libhts-dev/usr/share/man/man5/sam.5 debian/tabix/usr/share/man/man1/tabix.1
mv debian/libhts-dev/usr/share/man/man5/vcf.5.dh-new debian/libhts-dev/usr/share/man/man5/vcf.5
chmod 0644 -- debian/libhts-dev/usr/share/man/man5/faidx.5 debian/libhts-dev/usr/share/man/man5/vcf.5
dh_lintian -a
install -d debian/libhts2/usr/share/lintian/overrides
install -p -m0644 debian/libhts2.lintian-overrides debian/libhts2/usr/share/lintian/overrides/libhts2
install -d debian/tabix/usr/share/lintian/overrides
install -p -m0644 debian/tabix.lintian-overrides debian/tabix/usr/share/lintian/overrides/tabix
dh_perl -a
dh_link -a
rm -f debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.2
ln -s libhts.so.1.7-2 debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.2
rm -f debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so
ln -s libhts.so.1.7-2 debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so
rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz
ln -s tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz
dh_strip_nondeterminism -a
Using 1518610398 as canonical time
Normalizing debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.a using File::StripNondeterminism::handlers::ar
dh_compress -a
cd debian/libhts2
cd debian/libhts-dev
cd debian/tabix
chmod a-x usr/share/doc/libhts2/changelog usr/share/doc/libhts2/changelog.Debian
gzip -9nf usr/share/doc/libhts2/changelog usr/share/doc/libhts2/changelog.Debian
chmod a-x usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5
chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1
gzip -9nf usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5
gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1
cd '/<<PKGBUILDDIR>>'
cd '/<<PKGBUILDDIR>>'
cd '/<<PKGBUILDDIR>>'
dh_fixperms -a
find debian/libhts2 -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/libhts-dev -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/tabix -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/libhts2 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/tabix ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libhts2/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts2/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts2/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/libhts2/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/tabix/usr/share/man debian/tabix/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts-dev/usr/share/man debian/libhts-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts2 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian/libhts2/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/libhts-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
dh_missing -a
dh_strip -a
strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.a
install -d debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/b8
objcopy --only-keep-debug --compress-debug-sections debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.7-2 debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/b8/4ce5c7c61e740be389d7b8a73c17cff476cbb5.debug
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fc
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fc/10be4a0fc46fdc46c964832e461e489d8bf49f.debug
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fc/10be4a0fc46fdc46c964832e461e489d8bf49f.debug
chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fc/10be4a0fc46fdc46c964832e461e489d8bf49f.debug
strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip
objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fc/10be4a0fc46fdc46c964832e461e489d8bf49f.debug debian/tabix/usr/bin/bgzip
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cf
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cf/585a3a7e4cadbdcd4a3785beff98508aaf07e7.debug
chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/b8/4ce5c7c61e740be389d7b8a73c17cff476cbb5.debug
chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/b8/4ce5c7c61e740be389d7b8a73c17cff476cbb5.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.7-2
objcopy --add-gnu-debuglink debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/b8/4ce5c7c61e740be389d7b8a73c17cff476cbb5.debug debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.7-2
install -d debian/.debhelper/libhts2/dbgsym-root/usr/share/doc
ln -s libhts2 debian/.debhelper/libhts2/dbgsym-root/usr/share/doc/libhts2-dbgsym
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cf/585a3a7e4cadbdcd4a3785beff98508aaf07e7.debug
chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cf/585a3a7e4cadbdcd4a3785beff98508aaf07e7.debug
strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/htsfile
objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cf/585a3a7e4cadbdcd4a3785beff98508aaf07e7.debug debian/tabix/usr/bin/htsfile
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/bb
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/bb/13c21ede93c2ab59d0de6e9e660fabc7ddee72.debug
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/bb/13c21ede93c2ab59d0de6e9e660fabc7ddee72.debug
chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/bb/13c21ede93c2ab59d0de6e9e660fabc7ddee72.debug
strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/tabix
objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/bb/13c21ede93c2ab59d0de6e9e660fabc7ddee72.debug debian/tabix/usr/bin/tabix
install -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc
ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym
dh_makeshlibs -a
rm -f debian/libhts2/DEBIAN/shlibs
install -d debian/libhts2/DEBIAN
echo "libhts 2 libhts2" >> debian/libhts2/DEBIAN/shlibs
chmod 0644 -- debian/libhts2/DEBIAN/shlibs
chown 0:0 -- debian/libhts2/DEBIAN/shlibs
dpkg-gensymbols -plibhts2 -Idebian/libhts2.symbols -Pdebian/libhts2 -edebian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.7-2
mv debian/.debhelper/generated/libhts2/triggers.new debian/.debhelper/generated/libhts2/triggers
rm -f debian/libhts-dev/DEBIAN/shlibs
rm -f debian/tabix/DEBIAN/shlibs
dh_shlibdeps -a
dpkg-shlibdeps -Tdebian/libhts2.substvars debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.7-2
install -d debian/tabix/DEBIAN
dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/tabix were not linked against libm.so.6 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/tabix were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
install -p -m0644 debian/.debhelper/generated/libhts2/triggers debian/libhts2/DEBIAN/triggers
install -d debian/libhts-dev/DEBIAN
dh_gencontrol -a
echo misc:Depends= >> debian/libhts-dev.substvars
echo misc:Pre-Depends= >> debian/libhts-dev.substvars
dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -Pdebian/libhts-dev
echo misc:Depends= >> debian/libhts2.substvars
echo misc:Pre-Depends= >> debian/libhts2.substvars
install -d debian/.debhelper/libhts2/dbgsym-root/DEBIAN
dpkg-gencontrol -plibhts2 -ldebian/changelog -Tdebian/libhts2.substvars -Pdebian/.debhelper/libhts2/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=libhts2-dbgsym "-DDepends=libhts2 (= \${binary:Version})" "-DDescription=debug symbols for libhts2" -DBuild-Ids=b84ce5c7c61e740be389d7b8a73c17cff476cbb5 -DSection=debug -UReplaces -UBreaks
echo misc:Depends= >> debian/tabix.substvars
echo misc:Pre-Depends= >> debian/tabix.substvars
install -d debian/.debhelper/tabix/dbgsym-root/DEBIAN
dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/.debhelper/tabix/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=bb13c21ede93c2ab59d0de6e9e660fabc7ddee72 cf585a3a7e4cadbdcd4a3785beff98508aaf07e7 fc10be4a0fc46fdc46c964832e461e489d8bf49f" -DSection=debug -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control
chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control
dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix
chmod 0644 -- debian/libhts-dev/DEBIAN/control
chown 0:0 -- debian/libhts-dev/DEBIAN/control
chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/control
chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/control
dpkg-gencontrol -plibhts2 -ldebian/changelog -Tdebian/libhts2.substvars -Pdebian/libhts2
chmod 0644 -- debian/tabix/DEBIAN/control
chown 0:0 -- debian/tabix/DEBIAN/control
chmod 0644 -- debian/libhts2/DEBIAN/control
chown 0:0 -- debian/libhts2/DEBIAN/control
dh_md5sums -a
(cd debian/libhts2 >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
(cd debian/libhts-dev >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
(cd debian/tabix >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
chmod 0644 -- debian/libhts2/DEBIAN/md5sums
chown 0:0 -- debian/libhts2/DEBIAN/md5sums
(cd debian/.debhelper/libhts2/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums
chown 0:0 -- debian/libhts-dev/DEBIAN/md5sums
chmod 0644 -- debian/tabix/DEBIAN/md5sums
chown 0:0 -- debian/tabix/DEBIAN/md5sums
(cd debian/.debhelper/tabix/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/md5sums
chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums
chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --build debian/libhts2 ..
dpkg-deb --build debian/libhts-dev ..
dpkg-deb --build debian/.debhelper/tabix/dbgsym-root ..
dpkg-deb: building package 'libhts2' in '../libhts2_1.7-2_armhf.deb'.
dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.7-2_armhf.deb'.
dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.7-2_armhf.deb'.
dpkg-deb --build debian/.debhelper/libhts2/dbgsym-root ..
dpkg-deb: building package 'libhts2-dbgsym' in '../libhts2-dbgsym_1.7-2_armhf.deb'.
dpkg-deb --build debian/tabix ..
dpkg-deb: building package 'tabix' in '../tabix_1.7-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../htslib_1.7-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build htslib-1.7
dpkg-source: info: using options from htslib-1.7/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-02-19T04:45:14Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
htslib_1.7-2_armhf.changes:
---------------------------
Format: 1.8
Date: Wed, 14 Feb 2018 13:13:18 +0100
Source: htslib
Binary: libhts2 libhts-dev libhts-private-dev htslib-test tabix
Architecture: armhf
Version: 1.7-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
htslib-test - Test data for HTSlib
libhts-dev - development files for the HTSlib
libhts-private-dev - private development files for the HTSlib (use with care)
libhts2 - C library for high-throughput sequencing data formats
tabix - generic indexer for TAB-delimited genome position files
Closes: 890303
Changes:
htslib (1.7-2) unstable; urgency=medium
.
* Move all needed files into htslib-test package
Closes: #890303
* Document how to test the package
* Update symbols file
Checksums-Sha1:
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e6529b03891049697ba3fe46c378c2be247a7286 1830308 tabix-dbgsym_1.7-2_armhf.deb
aa3aa03929201f72042b6b95753a53ee1f653740 260276 tabix_1.7-2_armhf.deb
Checksums-Sha256:
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4be00020843dc6672964f2e97705c2a600ece58809057cf518444208436ef09f 328952 libhts-dev_1.7-2_armhf.deb
b8c4fd6a82981e62dc770320f67a9e5e7c6fe8b79b486b067535ddbde8de0f03 733276 libhts2-dbgsym_1.7-2_armhf.deb
42235e3d6bbc266dcca48909e886389ac6e929e97bc22ab6b26fe5c561ecb15f 259464 libhts2_1.7-2_armhf.deb
98f1f5f2c31643344475eda306280fcdffe0dfe575b54c4c31ce53df1a05d379 1830308 tabix-dbgsym_1.7-2_armhf.deb
8dd40cd6c182ce9f2656f1439802add270eded9f9d8be1070af1b3293fcd8417 260276 tabix_1.7-2_armhf.deb
Files:
2cacf0c04e842f0ffa29e114ade6f43c 5998 science optional htslib_1.7-2_armhf.buildinfo
2da7fb017f75505a392286accda4a5c8 328952 libdevel optional libhts-dev_1.7-2_armhf.deb
c5cfb49bdcbcfb4ddf59b271220a3366 733276 debug optional libhts2-dbgsym_1.7-2_armhf.deb
7a97970625fe8005913bf45135e7cddc 259464 libs optional libhts2_1.7-2_armhf.deb
253a16c8760be5b0b1066005a73c3134 1830308 debug optional tabix-dbgsym_1.7-2_armhf.deb
0359dfb090fb3306c6ceff147b433efb 260276 science optional tabix_1.7-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libhts-dev_1.7-2_armhf.deb
--------------------------
new Debian package, version 2.0.
size 328952 bytes: control archive=1856 bytes.
1032 bytes, 24 lines control
2259 bytes, 35 lines md5sums
Package: libhts-dev
Source: htslib
Version: 1.7-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1065
Depends: libhts2 (= 1.7-2), liblzma-dev
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/samtools/htslib
Description: development files for the HTSlib
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
Format), used for high-throughput sequencing data, and is the core library
used by samtools and bcftools. HTSlib only depends on zlib. It is known to be
compatible with gcc, g++ and clang.
.
HTSlib implements a generalized BAM (binary SAM) index, with file extension
‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
new index and then for the old if the new index is absent.
.
This package contains development files for the HTSlib: headers, static
library, manual pages, etc.
drwxr-xr-x root/root 0 2018-02-14 12:13 ./
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/include/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/include/htslib/
-rw-r--r-- root/root 14797 2018-01-26 12:01 ./usr/include/htslib/bgzf.h
-rw-r--r-- root/root 15393 2018-01-26 12:01 ./usr/include/htslib/cram.h
-rw-r--r-- root/root 5696 2018-01-26 12:01 ./usr/include/htslib/faidx.h
-rw-r--r-- root/root 9878 2018-01-26 12:01 ./usr/include/htslib/hfile.h
-rw-r--r-- root/root 29264 2018-01-26 12:01 ./usr/include/htslib/hts.h
-rw-r--r-- root/root 3336 2018-01-26 12:01 ./usr/include/htslib/hts_defs.h
-rw-r--r-- root/root 11446 2018-01-26 12:01 ./usr/include/htslib/hts_endian.h
-rw-r--r-- root/root 3890 2018-01-26 12:01 ./usr/include/htslib/hts_log.h
-rw-r--r-- root/root 1996 2018-01-26 12:01 ./usr/include/htslib/hts_os.h
-rw-r--r-- root/root 4195 2018-01-26 12:01 ./usr/include/htslib/kbitset.h
-rw-r--r-- root/root 2716 2018-01-26 12:01 ./usr/include/htslib/kfunc.h
-rw-r--r-- root/root 21540 2018-01-26 12:01 ./usr/include/htslib/khash.h
-rw-r--r-- root/root 3990 2018-01-26 12:01 ./usr/include/htslib/khash_str2int.h
-rw-r--r-- root/root 5086 2018-01-26 12:01 ./usr/include/htslib/klist.h
-rw-r--r-- root/root 2850 2018-01-26 12:01 ./usr/include/htslib/knetfile.h
-rw-r--r-- root/root 8900 2018-01-26 12:01 ./usr/include/htslib/kseq.h
-rw-r--r-- root/root 10488 2018-01-26 12:01 ./usr/include/htslib/ksort.h
-rw-r--r-- root/root 6933 2018-01-26 12:01 ./usr/include/htslib/kstring.h
-rw-r--r-- root/root 5834 2018-01-26 12:01 ./usr/include/htslib/regidx.h
-rw-r--r-- root/root 24161 2018-01-26 12:01 ./usr/include/htslib/sam.h
-rw-r--r-- root/root 14954 2018-01-26 12:01 ./usr/include/htslib/synced_bcf_reader.h
-rw-r--r-- root/root 3118 2018-01-26 12:01 ./usr/include/htslib/tbx.h
-rw-r--r-- root/root 9386 2018-01-26 12:01 ./usr/include/htslib/thread_pool.h
-rw-r--r-- root/root 43302 2018-01-26 12:01 ./usr/include/htslib/vcf.h
-rw-r--r-- root/root 1602 2018-01-26 12:01 ./usr/include/htslib/vcf_sweep.h
-rw-r--r-- root/root 4819 2018-01-26 12:01 ./usr/include/htslib/vcfutils.h
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 766258 2018-02-14 12:13 ./usr/lib/arm-linux-gnueabihf/libhts.a
lrwxrwxrwx root/root 0 2018-02-14 12:13 ./usr/lib/arm-linux-gnueabihf/libhts.so -> libhts.so.1.7-2
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 489 2018-02-14 12:13 ./usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/doc/libhts-dev/
-rw-r--r-- root/root 401 2018-02-14 12:13 ./usr/share/doc/libhts-dev/README.test
-rw-r--r-- root/root 3363 2018-02-14 12:13 ./usr/share/doc/libhts-dev/changelog.Debian.gz
-rw-r--r-- root/root 6159 2018-01-26 12:01 ./usr/share/doc/libhts-dev/changelog.gz
-rw-r--r-- root/root 5739 2018-02-14 12:13 ./usr/share/doc/libhts-dev/copyright
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/man/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/man/man5/
-rw-r--r-- root/root 2080 2018-02-14 12:13 ./usr/share/man/man5/faidx.5.gz
-rw-r--r-- root/root 1535 2018-02-14 12:13 ./usr/share/man/man5/sam.5.gz
-rw-r--r-- root/root 1854 2018-02-14 12:13 ./usr/share/man/man5/vcf.5.gz
libhts2-dbgsym_1.7-2_armhf.deb
------------------------------
new Debian package, version 2.0.
size 733276 bytes: control archive=548 bytes.
382 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libhts2-dbgsym
Source: htslib
Version: 1.7-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 776
Depends: libhts2 (= 1.7-2)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libhts2
Build-Ids: b84ce5c7c61e740be389d7b8a73c17cff476cbb5
drwxr-xr-x root/root 0 2018-02-14 12:13 ./
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/debug/.build-id/b8/
-rw-r--r-- root/root 784180 2018-02-14 12:13 ./usr/lib/debug/.build-id/b8/4ce5c7c61e740be389d7b8a73c17cff476cbb5.debug
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-02-14 12:13 ./usr/share/doc/libhts2-dbgsym -> libhts2
libhts2_1.7-2_armhf.deb
-----------------------
new Debian package, version 2.0.
size 259464 bytes: control archive=4760 bytes.
1044 bytes, 21 lines control
359 bytes, 5 lines md5sums
17 bytes, 1 lines shlibs
19917 bytes, 740 lines symbols
67 bytes, 2 lines triggers
Package: libhts2
Source: htslib
Version: 1.7-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 657
Depends: libbz2-1.0, libc6 (>= 2.23), libcurl3-gnutls (>= 7.18.0), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.2.0)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/samtools/htslib
Description: C library for high-throughput sequencing data formats
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
Format), used for high-throughput sequencing data, and is the core library
used by samtools and bcftools. HTSlib only depends on zlib. It is known to be
compatible with gcc, g++ and clang.
.
HTSlib implements a generalized BAM (binary SAM) index, with file extension
‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
new index and then for the old if the new index is absent.
drwxr-xr-x root/root 0 2018-02-14 12:13 ./
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 619948 2018-02-14 12:13 ./usr/lib/arm-linux-gnueabihf/libhts.so.1.7-2
lrwxrwxrwx root/root 0 2018-02-14 12:13 ./usr/lib/arm-linux-gnueabihf/libhts.so.2 -> libhts.so.1.7-2
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/doc/libhts2/
-rw-r--r-- root/root 3363 2018-02-14 12:13 ./usr/share/doc/libhts2/changelog.Debian.gz
-rw-r--r-- root/root 6159 2018-01-26 12:01 ./usr/share/doc/libhts2/changelog.gz
-rw-r--r-- root/root 5739 2018-02-14 12:13 ./usr/share/doc/libhts2/copyright
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/lintian/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 105 2018-02-14 12:13 ./usr/share/lintian/overrides/libhts2
tabix-dbgsym_1.7-2_armhf.deb
----------------------------
new Debian package, version 2.0.
size 1830308 bytes: control archive=656 bytes.
442 bytes, 12 lines control
318 bytes, 3 lines md5sums
Package: tabix-dbgsym
Source: htslib
Version: 1.7-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1954
Depends: tabix (= 1.7-2)
Section: debug
Priority: optional
Description: debug symbols for tabix
Build-Ids: bb13c21ede93c2ab59d0de6e9e660fabc7ddee72 cf585a3a7e4cadbdcd4a3785beff98508aaf07e7 fc10be4a0fc46fdc46c964832e461e489d8bf49f
drwxr-xr-x root/root 0 2018-02-14 12:13 ./
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/debug/.build-id/bb/
-rw-r--r-- root/root 703496 2018-02-14 12:13 ./usr/lib/debug/.build-id/bb/13c21ede93c2ab59d0de6e9e660fabc7ddee72.debug
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/debug/.build-id/cf/
-rw-r--r-- root/root 687824 2018-02-14 12:13 ./usr/lib/debug/.build-id/cf/585a3a7e4cadbdcd4a3785beff98508aaf07e7.debug
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/lib/debug/.build-id/fc/
-rw-r--r-- root/root 595344 2018-02-14 12:13 ./usr/lib/debug/.build-id/fc/10be4a0fc46fdc46c964832e461e489d8bf49f.debug
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-02-14 12:13 ./usr/share/doc/tabix-dbgsym -> tabix
tabix_1.7-2_armhf.deb
---------------------
new Debian package, version 2.0.
size 260276 bytes: control archive=1132 bytes.
942 bytes, 19 lines control
549 bytes, 9 lines md5sums
Package: tabix
Source: htslib
Version: 1.7-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1429
Depends: libbz2-1.0, libc6 (>= 2.15), libcurl3-gnutls (>= 7.18.0), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.2.0)
Section: science
Priority: optional
Homepage: https://github.com/samtools/htslib
Description: generic indexer for TAB-delimited genome position files
Tabix indexes files where some columns indicate sequence coordinates: name
(usually a chromosome), start and stop. The input data file must be position
sorted and compressed by bgzip (provided in this package), which has a gzip
like interface. After indexing, tabix is able to quickly retrieve data lines by
chromosomal coordinates. Fast data retrieval also works over network if an URI
is given as a file name.
.
This version of tabix is built from the HTSlib source.
drwxr-xr-x root/root 0 2018-02-14 12:13 ./
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/bin/
-rwxr-xr-x root/root 427480 2018-02-14 12:13 ./usr/bin/bgzip
-rwxr-xr-x root/root 493044 2018-02-14 12:13 ./usr/bin/htsfile
-rwxr-xr-x root/root 505328 2018-02-14 12:13 ./usr/bin/tabix
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/doc/tabix/
-rw-r--r-- root/root 3363 2018-02-14 12:13 ./usr/share/doc/tabix/changelog.Debian.gz
-rw-r--r-- root/root 6159 2018-01-26 12:01 ./usr/share/doc/tabix/changelog.gz
-rw-r--r-- root/root 5739 2018-02-14 12:13 ./usr/share/doc/tabix/copyright
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/lintian/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 186 2018-02-14 12:13 ./usr/share/lintian/overrides/tabix
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/man/
drwxr-xr-x root/root 0 2018-02-14 12:13 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2018-02-14 12:13 ./usr/share/man/man1/bgzip.1.gz -> tabix.1.gz
-rw-r--r-- root/root 1702 2018-02-14 12:13 ./usr/share/man/man1/htsfile.1.gz
-rw-r--r-- root/root 2820 2018-02-14 12:13 ./usr/share/man/man1/tabix.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 46632
Build-Time: 210
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 194
Job: htslib_1.7-2
Machine Architecture: armhf
Package: htslib
Package-Time: 419
Source-Version: 1.7-2
Space: 46632
Status: successful
Version: 1.7-2
--------------------------------------------------------------------------------
Finished at 2018-02-19T04:45:14Z
Build needed 00:06:59, 46632k disk space