htslib →
1.9-12~deb10u1 →
armhf → 2021-10-10 21:22:56
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| htslib 1.9-12~deb10u1 (armhf) Sun, 10 Oct 2021 20:52:00 +0000 |
+==============================================================================+
Package: htslib
Version: 1.9-12~deb10u1
Source Version: 1.9-12~deb10u1
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-9a2dd171-27d7-4e2c-aae3-7dece1e9a1f2' 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 [11.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.0 MB]
Fetched 24.4 MB in 26s (946 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://salsa.debian.org/med-team/htslib.git
Please use:
git clone https://salsa.debian.org/med-team/htslib.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1303 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main htslib 1.9-12~deb10u1 (dsc) [2415 B]
Get:2 http://172.17.0.1/private buster-staging/main htslib 1.9-12~deb10u1 (tar) [1286 kB]
Get:3 http://172.17.0.1/private buster-staging/main htslib 1.9-12~deb10u1 (diff) [15.0 kB]
Fetched 1303 kB in 0s (3754 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/htslib-lrpqGh/htslib-1.9' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/htslib-lrpqGh' 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-cZ8Img/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-cZ8Img/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-cZ8Img/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-cZ8Img/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-cZ8Img/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-cZ8Img/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-cZ8Img/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-cZ8Img/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2848 B/s)
Reading package lists...
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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 3 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-cZ8Img/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
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(Reading database ... 12059 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 (>= 11~), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev
Filtered Build-Depends: debhelper (>= 11~), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev
dpkg-deb: building package 'sbuild-build-depends-htslib-dummy' in '/<<BUILDDIR>>/resolver-cZ8Img/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-cZ8Img/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-cZ8Img/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-cZ8Img/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-cZ8Img/apt_archive ./ Sources [540 B]
Get:5 copy:/<<BUILDDIR>>/resolver-cZ8Img/apt_archive ./ Packages [616 B]
Fetched 2489 B in 1s (3140 B/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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
libcurl3-gnutls libcurl4-gnutls-dev libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libicu63
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc
libmagic1 libncurses6 libnghttp2-14 libpipeline1 libpsl5 librtmp1
libsigsegv2 libssh2-1 libssl-dev libssl1.1 libtinfo5 libtool libuchardet0
libxml2 m4 man-db po-debconf sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev pkg-config krb5-doc krb5-user liblzma-doc
libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor
less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl
libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2
publicsuffix 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 dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
libcurl3-gnutls libcurl4-gnutls-dev libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libicu63
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc
libmagic1 libncurses6 libnghttp2-14 libpipeline1 libpsl5 librtmp1
libsigsegv2 libssh2-1 libssl-dev libssl1.1 libtinfo5 libtool libuchardet0
libxml2 m4 man-db po-debconf sbuild-build-depends-htslib-dummy
sensible-utils zlib1g-dev
0 upgraded, 54 newly installed, 0 to remove and 3 not upgraded.
Need to get 23.3 MB of archives.
After this operation, 80.9 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-cZ8Img/apt_archive ./ sbuild-build-depends-htslib-dummy 0.invalid.0 [900 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-2+deb10u1 [105 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libtinfo5 armhf 6.1+20181013-2+deb10u2 [309 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-3+deb10u1 [782 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-2 [1230 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.35-4+deb10u2 [242 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.35-4+deb10u2 [110 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.35-4+deb10u2 [65.5 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1078 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-6+deb10u1 [7973 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+deb10u2 [572 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [78.9 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf debhelper all 12.1.1 [1016 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-9.2~deb10u1 [27.7 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.17-3+deb10u2 [62.4 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.17-3+deb10u2 [118 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libssl1.1 armhf 1.1.1d-0+deb10u7 [1263 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.17-3+deb10u2 [319 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.17-3+deb10u2 [136 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.36.0-2+deb10u1 [73.7 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.64.0-4+deb10u2 [292 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libcurl4-gnutls-dev armhf 7.64.0-4+deb10u2 [365 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libdeflate0 armhf 1.2-1 [48.4 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libdeflate-dev armhf 1.2-1 [42.0 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.1d-0+deb10u7 [1567 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23.1 [25.1 kB]
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Unpacking libkrb5support0:armhf (1.17-3+deb10u2) ...
Selecting previously unselected package libk5crypto3:armhf.
Preparing to unpack .../37-libk5crypto3_1.17-3+deb10u2_armhf.deb ...
Unpacking libk5crypto3:armhf (1.17-3+deb10u2) ...
Selecting previously unselected package libssl1.1:armhf.
Preparing to unpack .../38-libssl1.1_1.1.1d-0+deb10u7_armhf.deb ...
Unpacking libssl1.1:armhf (1.1.1d-0+deb10u7) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../39-libkrb5-3_1.17-3+deb10u2_armhf.deb ...
Unpacking libkrb5-3:armhf (1.17-3+deb10u2) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
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Unpacking libgssapi-krb5-2:armhf (1.17-3+deb10u2) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../41-libnghttp2-14_1.36.0-2+deb10u1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.36.0-2+deb10u1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../42-libpsl5_0.20.2-2_armhf.deb ...
Unpacking libpsl5:armhf (0.20.2-2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../43-librtmp1_2.4+20151223.gitfa8646d.1-2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../44-libssh2-1_1.8.0-2.1_armhf.deb ...
Unpacking libssh2-1:armhf (1.8.0-2.1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../45-libcurl3-gnutls_7.64.0-4+deb10u2_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.64.0-4+deb10u2) ...
Selecting previously unselected package libcurl4-gnutls-dev:armhf.
Preparing to unpack .../46-libcurl4-gnutls-dev_7.64.0-4+deb10u2_armhf.deb ...
Unpacking libcurl4-gnutls-dev:armhf (7.64.0-4+deb10u2) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../47-libdeflate0_1.2-1_armhf.deb ...
Unpacking libdeflate0:armhf (1.2-1) ...
Selecting previously unselected package libdeflate-dev:armhf.
Preparing to unpack .../48-libdeflate-dev_1.2-1_armhf.deb ...
Unpacking libdeflate-dev:armhf (1.2-1) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../49-liblzma-dev_5.2.4-1_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.4-1) ...
Selecting previously unselected package libssl-dev:armhf.
Preparing to unpack .../50-libssl-dev_1.1.1d-0+deb10u7_armhf.deb ...
Unpacking libssl-dev:armhf (1.1.1d-0+deb10u7) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../51-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Selecting previously unselected package dh-exec.
Preparing to unpack .../52-dh-exec_0.23.1_armhf.deb ...
Unpacking dh-exec (0.23.1) ...
Selecting previously unselected package sbuild-build-depends-htslib-dummy.
Preparing to unpack .../53-sbuild-build-depends-htslib-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.1-2) ...
Setting up libkeyutils1:armhf (1.6-6) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up libmagic-mgc (1:5.35-4+deb10u2) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1d-0+deb10u7) ...
Setting up libnghttp2-14:armhf (1.36.0-2+deb10u1) ...
Setting up libmagic1:armhf (1:5.35-4+deb10u2) ...
Setting up libdeflate0:armhf (1.2-1) ...
Setting up gettext-base (0.19.8.1-9) ...
Setting up file (1:5.35-4+deb10u2) ...
Setting up libicu63:armhf (63.1-6+deb10u1) ...
Setting up libkrb5support0:armhf (1.17-3+deb10u2) ...
Setting up autotools-dev (20180224.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libssl-dev:armhf (1.1.1d-0+deb10u7) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up libk5crypto3:armhf (1.17-3+deb10u2) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up sensible-utils (0.0.12) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-3+deb10u2) ...
Setting up libbsd0:armhf (0.9.1-2+deb10u1) ...
Setting up libtinfo5:armhf (6.1+20181013-2+deb10u2) ...
Setting up libdeflate-dev:armhf (1.2-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+deb10u2) ...
Setting up libbz2-dev:armhf (1.0.6-9.2~deb10u1) ...
Setting up libfile-stripnondeterminism-perl (1.1.2-1) ...
Setting up libtool (2.4.6-9) ...
Setting up m4 (1.4.18-2) ...
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 libgssapi-krb5-2:armhf (1.17-3+deb10u2) ...
Setting up libcroco3:armhf (0.6.12-3) ...
Setting up autoconf (2.69-11) ...
Setting up dwz (0.12-3) ...
Setting up groff-base (1.22.4-3+deb10u1) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-9) ...
Setting up libcurl3-gnutls:armhf (7.64.0-4+deb10u2) ...
Setting up libcurl4-gnutls-dev:armhf (7.64.0-4+deb10u2) ...
Setting up man-db (2.8.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.1.2-1) ...
Setting up debhelper (12.1.1) ...
Setting up dh-exec (0.23.1) ...
Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-10+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-16+rpi2 dpkg-dev_1.19.7 g++-8_8.3.0-6+rpi1 gcc-8_8.3.0-6+rpi1 libc6-dev_2.28-10+rpi1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.2.3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3+rpi1+deb10u10 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16+rpi2 binutils-arm-linux-gnueabihf_2.31.1-16+rpi2 binutils-common_2.31.1-16+rpi2 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9.2~deb10u1 coreutils_8.30-3 cpp_4:8.3.0-1+rpi2 cpp-8_8.3.0-6+rpi1 dash_0.5.10.2-5 debconf_1.5.71 debhelper_12.1.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-exec_0.23.1 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-3 dirmngr_2.2.12-1+rpi1+deb10u1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.12-3 e2fsprogs_1.44.5-1+deb10u3 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-4+deb10u2 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1+rpi2 g++-8_8.3.0-6+rpi1 gcc_4:8.3.0-1+rpi2 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b1 gcc-7-base_7.3.0-19 gcc-8_8.3.0-6+rpi1 gcc-8-base_8.3.0-6+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1+deb10u1 gnupg-l10n_2.2.12-1+rpi1+deb10u1 gnupg-utils_2.2.12-1+rpi1+deb10u1 gpg_2.2.12-1+rpi1+deb10u1 gpg-agent_2.2.12-1+rpi1+deb10u1 gpg-wks-client_2.2.12-1+rpi1+deb10u1 gpg-wks-server_2.2.12-1+rpi1+deb10u1 gpgconf_2.2.12-1+rpi1+deb10u1 gpgsm_2.2.12-1+rpi1+deb10u1 gpgv_2.2.12-1+rpi1+deb10u1 grep_3.3-1 groff-base_1.22.4-3+deb10u1 gzip_1.9-3 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2.3 libarchive-zip-perl_1.64-1 libasan5_8.3.0-6+rpi1 libassuan0_2.5.2-1 libatomic1_8.3.0-6+rpi1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16+rpi2 libblkid1_2.33.1-0.1 libbsd0_0.9.1-2+deb10u1 libbz2-1.0_1.0.6-9.2~deb10u1 libbz2-dev_1.0.6-9.2~deb10u1 libc-bin_2.28-10+rpi1 libc-dev-bin_2.28-10+rpi1 libc6_2.28-10+rpi1 libc6-dev_2.28-10+rpi1 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-6+rpi1 libcom-err2_1.44.5-1+deb10u3 libcroco3_0.6.12-3 libcurl3-gnutls_7.64.0-4+deb10u2 libcurl4-gnutls-dev_7.64.0-4+deb10u2 libdb5.3_5.3.28+dfsg1-0.5 libdebconfclient0_0.249 libdeflate-dev_1.2-1 libdeflate0_1.2-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.44.5-1+deb10u3 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.2-1 libfl2_2.6.4-6.2 libgcc-8-dev_8.3.0-6+rpi1 libgcc1_1:8.3.0-6+rpi1 libgcrypt20_1.8.4-5+deb10u1 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libglib2.0-0_2.58.3-2+deb10u2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-4+deb10u7 libgomp1_8.3.0-6+rpi1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-3+deb10u2 libhogweed4_3.4.1-1+deb10u1 libicu63_63.1-6+deb10u1 libidn2-0_2.0.5-1+deb10u1 libisl19_0.20-2 libk5crypto3_1.17-3+deb10u2 libkeyutils1_1.6-6 libkrb5-3_1.17-3+deb10u2 libkrb5support0_1.17-3+deb10u2 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1+deb10u6 libldap-common_2.4.47+dfsg-3+rpi1+deb10u6 liblocale-gettext-perl_1.07-3+b3 liblz4-1_1.8.3-1+deb10u1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4+deb10u2 libmagic1_1:5.35-4+deb10u2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.1+20181013-2+deb10u2 libncursesw6_6.1+20181013-2+deb10u2 libnettle6_3.4.1-1+deb10u1 libnghttp2-14_1.36.0-2+deb10u1 libnpth0_1.6-1 libp11-kit0_0.23.15-2+deb10u1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpsl5_0.20.2-2 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1+deb10u1 libsasl2-modules-db_2.1.27+dfsg-1+deb10u1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.27.2-3+deb10u1 libss2_1.44.5-1+deb10u3 libssh2-1_1.8.0-2.1 libssl-dev_1.1.1d-0+deb10u7 libssl1.1_1.1.1d-0+deb10u7 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 libsystemd0_241-7~deb10u8+rpi1 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1+b1 libtext-iconv-perl_1.7-5+b10 libtext-wrapi18n-perl_0.06-7.1 libtinfo5_6.1+20181013-2+deb10u2 libtinfo6_6.1+20181013-2+deb10u2 libtool_2.4.6-9 libubsan1_8.3.0-6+rpi1 libuchardet0_0.0.6-3 libudev1_241-7~deb10u8+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+deb10u2 libzstd1_1.3.8+dfsg-3+rpi1+deb10u2 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2019051400+rpi1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2+deb10u2 ncurses-bin_6.1+20181013-2+deb10u2 netbase_5.6 passwd_1:4.5-1.1 patch_2.7.6-3+deb10u1 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6+deb10u1 pinentry-curses_1.1.0-2 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2021a-0+deb10u1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Jul 18 19:35:03 2021 UTC
gpgv: using RSA key EBF30A30A8D9C63BDA44C6945FB33F9359E9ED08
gpgv: issuer "anbe@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./htslib_1.9-12~deb10u1.dsc
dpkg-source: info: extracting htslib in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking htslib_1.9.orig.tar.gz
dpkg-source: info: unpacking htslib_1.9-12~deb10u1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying no_git_version
dpkg-source: info: applying define_PATH_MAX.patch
dpkg-source: info: applying fPIC.patch
dpkg-source: info: applying testShebang.patch
dpkg-source: info: applying fix_float_precision
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-9a2dd171-27d7-4e2c-aae3-7dece1e9a1f2
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package htslib
dpkg-buildpackage: info: source version 1.9-12~deb10u1
dpkg-buildpackage: info: source distribution buster
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from htslib-1.9/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
make -j4 distclean
make[2]: 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_realn 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[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -rf test_backup/
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
grep -q ^XDT_ configure.ac
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 --enable-gcs --enable-s3
./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 --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3
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 libdeflate.h... yes
checking for libdeflate_deflate_compress in -ldeflate... 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)" \
PACKAGE_VERSION="1.9-12~deb10u1" \
libdir=/usr/lib/arm-linux-gnueabihf
make -j4 "CFLAGS=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto" PACKAGE_VERSION=1.9-12\~deb10u1 libdir=/usr/lib/arm-linux-gnueabihf
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.9-12~deb10u1"' > version.h
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -flto -flto -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 -Wl,-flto -Wl,-flto -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 -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/hts_endian test/hts_endian.o -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto
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 -Wl,-flto -Wl,-flto -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/hfile test/hfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/sam test/sam.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_realn test/test_realn.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_view test/test_view.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
ln -sf libhts.so libhts.so.2
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -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>>'
echo '#define HTS_VERSION "1.9"' > version.h
gcc -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
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 -Wl,-flto -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o test/hfile test/hfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o test/sam test/sam.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o test/test_realn test/test_realn.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o test/test_view test/test_view.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
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/fastqs.fq
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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t auxf.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c2.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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#1000.sam, ref ce.fa:
./test_view -S -b ce#1000.sam > ce#1000.tmp.bam
./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam
./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram
./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
./test_view -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam
./test_view ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram
./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
./test_view -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam
./test_view ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
./test_view ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t md.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t auxf.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t c2.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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#1000.sam, ref ce.fa:
./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam
./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam
./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
./test_view -@4 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam
./test_view -@4 ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
./test_view -@4 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam
./test_view -@4 ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
./test_view -@4 ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t md.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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 -S -l0 -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 -o VERSION=2.1 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=2.1 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 -l0 -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 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 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_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
test_vcf_api:
/<<PKGBUILDDIR>>/test/test-vcf-api /tmp/YfrRbG0KOh/test-vcf-api.bcf
.. ok
test_vcf_sweep:
/<<PKGBUILDDIR>>/test/test-vcf-sweep /tmp/YfrRbG0KOh/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/YfrRbG0KOh -s 555287786
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/YfrRbG0KOh -s 1568061148
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/YfrRbG0KOh -s 387427099
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/YfrRbG0KOh -s 530380303
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/YfrRbG0KOh -s 431207944
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/YfrRbG0KOh -s 1521211038
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/YfrRbG0KOh -s 784902802
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/YfrRbG0KOh -s 790332009
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/YfrRbG0KOh -s 627763761
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/YfrRbG0KOh -s 1177178990
.. ok
test_command:
/<<PKGBUILDDIR>>/test/test-bcf-translate -
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/YfrRbG0KOh/headernul0.bam
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/YfrRbG0KOh/headernul1.bam
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/YfrRbG0KOh/headernul678.bam
.. ok
test_rebgzip: Alternate zlib/deflate library detected
test_rebgzip:
/<<PKGBUILDDIR>>/bgzip -I /<<PKGBUILDDIR>>/test/bgziptest.txt.tmp.gz.gzi -c -g /<<PKGBUILDDIR>>/test/bgziptest.txt
.. ok
test-logging:
/<<PKGBUILDDIR>>/test/test-logging.pl
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -f /<<PKGBUILDDIR>>/test/realn01.fa -i /<<PKGBUILDDIR>>/test/realn01.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -a -f /<<PKGBUILDDIR>>/test/realn01.fa -i /<<PKGBUILDDIR>>/test/realn01.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -a -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -e -f /<<PKGBUILDDIR>>/test/realn01.fa -i /<<PKGBUILDDIR>>/test/realn01.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -e -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -r -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02-r.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -a -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02_exp.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02_exp-a.sam -o -
.. ok
Number of tests:
total .. 97
passed .. 97
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
install -d /<<PKGBUILDDIR>>/debian/tmp
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
make[2]: Entering directory '/<<PKGBUILDDIR>>'
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 -flto -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
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/arm-linux-gnueabihf#g;s#@-PACKAGE_VERSION@#1.9#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
gcc -shared -Wl,-soname,libhts.so.2 -Wl,-z,relro -Wl,-z,now -Wl,-flto -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 -ldeflate -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.1.9
ln -sf libhts.so.1.9 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so
ln -sf libhts.so.1.9 /<<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 bgzip.1 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.1.9 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
cp --reflink=auto -a ./README 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/tabix/usr/share/doc/tabix/changelog.Debian
install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/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
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/vcf.5 > debian/libhts-dev/usr/share/man/man5/vcf.5.dh-new
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/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1
chmod 0644 -- 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
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/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/sam.5 > debian/libhts-dev/usr/share/man/man5/sam.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/libhts-dev/usr/share/man/man5/vcf.5 debian/tabix/usr/share/man/man1/htsfile.1
mv debian/libhts-dev/usr/share/man/man5/sam.5.dh-new debian/libhts-dev/usr/share/man/man5/sam.5
chmod 0644 -- debian/libhts-dev/usr/share/man/man5/faidx.5 debian/libhts-dev/usr/share/man/man5/sam.5
dh_perl -a
dh_link -a
rm -f debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.2
ln -s libhts.so.1.9 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.1.9 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
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
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
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
gzip -9nf usr/share/doc/libhts2/changelog usr/share/doc/libhts2/changelog.Debian
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
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
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/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/libhts2/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/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts2 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -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/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
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 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -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/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
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e7
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e7/81fbfa0bd6456452fe8340edd191af9a359a2a.debug
install -d debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/0b
objcopy --only-keep-debug --compress-debug-sections debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.9 debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/0b/01e928b76ad0efd3357f3afe7b9e79c328d062.debug
strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.a
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e7/81fbfa0bd6456452fe8340edd191af9a359a2a.debug
chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e7/81fbfa0bd6456452fe8340edd191af9a359a2a.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/e7/81fbfa0bd6456452fe8340edd191af9a359a2a.debug debian/tabix/usr/bin/bgzip
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/kfunc.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/knetfile.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/kstring.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/bcf_sr_sort.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/bgzf.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/errmod.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/faidx.o: plugin needed to handle lto object
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/9f
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/9f/bf1dbb535484d41e0253396161409ea85a6004.debug
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/hfile.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/hfile_net.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/hts.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/hts_os.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/md5.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/multipart.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/probaln.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/realn.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/regidx.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/sam.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/synced_bcf_reader.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/vcf_sweep.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/tbx.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/textutils.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/thread_pool.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/vcf.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/vcfutils.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/cram_codecs.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/cram_decode.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/cram_encode.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/cram_external.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/cram_index.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/cram_io.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/cram_samtools.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/cram_stats.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/files.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/mFILE.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/open_trace_file.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/pooled_alloc.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/rANS_static.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/sam_header.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/string_alloc.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/hfile_libcurl.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/hfile_gcs.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/st0p5XGB/hfile_s3.o: plugin needed to handle lto object
chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/0b/01e928b76ad0efd3357f3afe7b9e79c328d062.debug
chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/0b/01e928b76ad0efd3357f3afe7b9e79c328d062.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.9
objcopy --add-gnu-debuglink debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/0b/01e928b76ad0efd3357f3afe7b9e79c328d062.debug debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.9
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/9f/bf1dbb535484d41e0253396161409ea85a6004.debug
chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/9f/bf1dbb535484d41e0253396161409ea85a6004.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/9f/bf1dbb535484d41e0253396161409ea85a6004.debug debian/tabix/usr/bin/htsfile
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/f1
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/f1/a68879f1b47293a77ec53b87f18a0a63bb8f4e.debug
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/f1/a68879f1b47293a77ec53b87f18a0a63bb8f4e.debug
chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/f1/a68879f1b47293a77ec53b87f18a0a63bb8f4e.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/f1/a68879f1b47293a77ec53b87f18a0a63bb8f4e.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.1.9
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.1.9
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/tabix debian/tabix/usr/bin/bgzip were not linked against ld-linux-armhf.so.3 (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/tabix debian/tabix/usr/bin/bgzip were not linked against libm.so.6 (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/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=9fbf1dbb535484d41e0253396161409ea85a6004 e781fbfa0bd6456452fe8340edd191af9a359a2a f1a68879f1b47293a77ec53b87f18a0a63bb8f4e" -DSection=debug -UReplaces -UBreaks
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=0b01e928b76ad0efd3357f3afe7b9e79c328d062 -DSection=debug -UReplaces -UBreaks
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/libhts-dev/DEBIAN/control
chown 0:0 -- debian/libhts-dev/DEBIAN/control
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/libhts2/DEBIAN/control
chown 0:0 -- debian/libhts2/DEBIAN/control
chmod 0644 -- debian/tabix/DEBIAN/control
chown 0:0 -- debian/tabix/DEBIAN/control
dh_md5sums -a
cd debian/libhts2 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/libhts2/DEBIAN/md5sums
chown 0:0 -- debian/libhts2/DEBIAN/md5sums
chmod 0644 -- debian/tabix/DEBIAN/md5sums
chown 0:0 -- debian/tabix/DEBIAN/md5sums
cd debian/.debhelper/libhts2/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
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
chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums
chown 0:0 -- debian/libhts-dev/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_1.9-12~deb10u1_armhf.deb'.
dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.9-12~deb10u1_armhf.deb'.
dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.9-12~deb10u1_armhf.deb'.
dpkg-deb --build debian/.debhelper/libhts2/dbgsym-root ..
dpkg-deb: building package 'libhts2-dbgsym' in '../libhts2-dbgsym_1.9-12~deb10u1_armhf.deb'.
dpkg-deb --build debian/tabix ..
dpkg-deb: building package 'tabix' in '../tabix_1.9-12~deb10u1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../htslib_1.9-12~deb10u1_armhf.changes
dpkg-genchanges: warning: the current version (1.9-12~deb10u1) is earlier than the previous one (1.9-12)
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-source: info: using options from htslib-1.9/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 2021-10-10T21:22:45Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
htslib_1.9-12~deb10u1_armhf.changes:
------------------------------------
Format: 1.8
Date: Sun, 18 Jul 2021 21:31:48 +0200
Source: htslib
Binary: libhts-dev libhts2 libhts2-dbgsym tabix tabix-dbgsym
Architecture: armhf
Version: 1.9-12~deb10u1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Beckmann <anbe@debian.org>
Description:
libhts-dev - development files for the HTSlib
libhts2 - C library for high-throughput sequencing data formats
tabix - generic indexer for TAB-delimited genome position files
Changes:
htslib (1.9-12~deb10u1) buster; urgency=medium
.
* Rebuild for buster.
Checksums-Sha1:
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63f545f63480a386b7f76a1ba37b538289417ec9 217848 libhts2-dbgsym_1.9-12~deb10u1_armhf.deb
d54d654671843374f93ed490189daf81eba2f270 254436 libhts2_1.9-12~deb10u1_armhf.deb
411b6a8274fec6fb45a348071c231b191e606118 512720 tabix-dbgsym_1.9-12~deb10u1_armhf.deb
e422ae922f8fe9c0893eb00d6e3aa0d72e73e821 240808 tabix_1.9-12~deb10u1_armhf.deb
Checksums-Sha256:
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ab0cba9bbad5b407052b7c8cefd2fa126ee7f5aa6810406404384ddfd35864c4 4286740 libhts-dev_1.9-12~deb10u1_armhf.deb
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f5e98db3bb0d0c0bbaf5ff4ea4e49215044c925601598aa7eb81c9d785ef59da 512720 tabix-dbgsym_1.9-12~deb10u1_armhf.deb
1e84379f464efd9444f2e8246e80e5718a92f4446bcddc7f087d99b84973a9e2 240808 tabix_1.9-12~deb10u1_armhf.deb
Files:
c96fa0891a01b8bfba642c1818814bff 6531 science optional htslib_1.9-12~deb10u1_armhf.buildinfo
e5ec5f50673a8dde0445764c3a52eeec 4286740 libdevel optional libhts-dev_1.9-12~deb10u1_armhf.deb
db1d23d8c0b958383462831d5c52c4ff 217848 debug optional libhts2-dbgsym_1.9-12~deb10u1_armhf.deb
788a4791f503db9a1167be764c4e5085 254436 libs optional libhts2_1.9-12~deb10u1_armhf.deb
aa7a54c4e8f80a06dcf5458ac532834b 512720 debug optional tabix-dbgsym_1.9-12~deb10u1_armhf.deb
7e69ccb192688fcc1e7403bc59c1bd8c 240808 science optional tabix_1.9-12~deb10u1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libhts-dev_1.9-12~deb10u1_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 4286740 bytes: control archive=1892 bytes.
1062 bytes, 24 lines control
2325 bytes, 36 lines md5sums
Package: libhts-dev
Source: htslib
Version: 1.9-12~deb10u1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5133
Depends: libhts2 (= 1.9-12~deb10u1), liblzma-dev, zlib1g-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 2021-07-18 19:31 ./
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/include/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/include/htslib/
-rw-r--r-- root/root 14797 2018-07-18 08:33 ./usr/include/htslib/bgzf.h
-rw-r--r-- root/root 15393 2018-07-18 08:33 ./usr/include/htslib/cram.h
-rw-r--r-- root/root 8972 2018-07-18 08:33 ./usr/include/htslib/faidx.h
-rw-r--r-- root/root 10077 2018-07-18 08:33 ./usr/include/htslib/hfile.h
-rw-r--r-- root/root 30459 2018-07-18 08:33 ./usr/include/htslib/hts.h
-rw-r--r-- root/root 3336 2018-07-18 08:33 ./usr/include/htslib/hts_defs.h
-rw-r--r-- root/root 11446 2018-07-18 08:33 ./usr/include/htslib/hts_endian.h
-rw-r--r-- root/root 3898 2018-07-18 08:33 ./usr/include/htslib/hts_log.h
-rw-r--r-- root/root 1996 2018-07-18 08:33 ./usr/include/htslib/hts_os.h
-rw-r--r-- root/root 4195 2018-07-18 08:33 ./usr/include/htslib/kbitset.h
-rw-r--r-- root/root 2716 2018-07-18 08:33 ./usr/include/htslib/kfunc.h
-rw-r--r-- root/root 21540 2018-07-18 08:33 ./usr/include/htslib/khash.h
-rw-r--r-- root/root 3990 2018-07-18 08:33 ./usr/include/htslib/khash_str2int.h
-rw-r--r-- root/root 5086 2018-07-18 08:33 ./usr/include/htslib/klist.h
-rw-r--r-- root/root 2850 2018-07-18 08:33 ./usr/include/htslib/knetfile.h
-rw-r--r-- root/root 9139 2018-07-18 08:33 ./usr/include/htslib/kseq.h
-rw-r--r-- root/root 10567 2018-07-18 08:33 ./usr/include/htslib/ksort.h
-rw-r--r-- root/root 7012 2018-07-18 08:33 ./usr/include/htslib/kstring.h
-rw-r--r-- root/root 5834 2018-07-18 08:33 ./usr/include/htslib/regidx.h
-rw-r--r-- root/root 29580 2018-07-18 08:33 ./usr/include/htslib/sam.h
-rw-r--r-- root/root 14954 2018-07-18 08:33 ./usr/include/htslib/synced_bcf_reader.h
-rw-r--r-- root/root 3118 2018-07-18 08:33 ./usr/include/htslib/tbx.h
-rw-r--r-- root/root 9386 2018-07-18 08:33 ./usr/include/htslib/thread_pool.h
-rw-r--r-- root/root 43671 2018-07-18 08:33 ./usr/include/htslib/vcf.h
-rw-r--r-- root/root 1602 2018-07-18 08:33 ./usr/include/htslib/vcf_sweep.h
-rw-r--r-- root/root 4819 2018-07-18 08:33 ./usr/include/htslib/vcfutils.h
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 4919504 2021-07-18 19:31 ./usr/lib/arm-linux-gnueabihf/libhts.a
lrwxrwxrwx root/root 0 2021-07-18 19:31 ./usr/lib/arm-linux-gnueabihf/libhts.so -> libhts.so.1.9
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 583 2021-07-18 19:31 ./usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/doc/libhts-dev/
-rw-r--r-- root/root 273 2018-07-18 08:33 ./usr/share/doc/libhts-dev/README
-rw-r--r-- root/root 401 2019-09-04 08:27 ./usr/share/doc/libhts-dev/README.test
-rw-r--r-- root/root 4453 2021-07-18 19:31 ./usr/share/doc/libhts-dev/changelog.Debian.gz
-rw-r--r-- root/root 8097 2018-07-18 08:33 ./usr/share/doc/libhts-dev/changelog.gz
-rw-r--r-- root/root 5762 2019-09-04 08:27 ./usr/share/doc/libhts-dev/copyright
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/man/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/man/man5/
-rw-r--r-- root/root 2452 2021-07-18 19:31 ./usr/share/man/man5/faidx.5.gz
-rw-r--r-- root/root 1535 2021-07-18 19:31 ./usr/share/man/man5/sam.5.gz
-rw-r--r-- root/root 1854 2021-07-18 19:31 ./usr/share/man/man5/vcf.5.gz
libhts2-dbgsym_1.9-12~deb10u1_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 217848 bytes: control archive=560 bytes.
400 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libhts2-dbgsym
Source: htslib
Version: 1.9-12~deb10u1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 309
Depends: libhts2 (= 1.9-12~deb10u1)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libhts2
Build-Ids: 0b01e928b76ad0efd3357f3afe7b9e79c328d062
drwxr-xr-x root/root 0 2021-07-18 19:31 ./
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/debug/.build-id/0b/
-rw-r--r-- root/root 305432 2021-07-18 19:31 ./usr/lib/debug/.build-id/0b/01e928b76ad0efd3357f3afe7b9e79c328d062.debug
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-07-18 19:31 ./usr/share/doc/libhts2-dbgsym -> libhts2
libhts2_1.9-12~deb10u1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 254436 bytes: control archive=4812 bytes.
1133 bytes, 22 lines control
287 bytes, 4 lines md5sums
17 bytes, 1 lines shlibs
20119 bytes, 747 lines symbols
67 bytes, 2 lines triggers
Package: libhts2
Source: htslib
Version: 1.9-12~deb10u1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 624
Depends: libbz2-1.0, libc6 (>= 2.23), libcurl3-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.2.0)
Breaks: python-pysam (<< 0.15~), python3-pysam (<< 0.15~)
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 2021-07-18 19:31 ./
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 587180 2021-07-18 19:31 ./usr/lib/arm-linux-gnueabihf/libhts.so.1.9
lrwxrwxrwx root/root 0 2021-07-18 19:31 ./usr/lib/arm-linux-gnueabihf/libhts.so.2 -> libhts.so.1.9
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/doc/libhts2/
-rw-r--r-- root/root 4453 2021-07-18 19:31 ./usr/share/doc/libhts2/changelog.Debian.gz
-rw-r--r-- root/root 8097 2018-07-18 08:33 ./usr/share/doc/libhts2/changelog.gz
-rw-r--r-- root/root 5762 2019-09-04 08:27 ./usr/share/doc/libhts2/copyright
tabix-dbgsym_1.9-12~deb10u1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 512720 bytes: control archive=664 bytes.
459 bytes, 12 lines control
318 bytes, 3 lines md5sums
Package: tabix-dbgsym
Source: htslib
Version: 1.9-12~deb10u1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 683
Depends: tabix (= 1.9-12~deb10u1)
Section: debug
Priority: optional
Description: debug symbols for tabix
Build-Ids: 9fbf1dbb535484d41e0253396161409ea85a6004 e781fbfa0bd6456452fe8340edd191af9a359a2a f1a68879f1b47293a77ec53b87f18a0a63bb8f4e
drwxr-xr-x root/root 0 2021-07-18 19:31 ./
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/debug/.build-id/9f/
-rw-r--r-- root/root 241024 2021-07-18 19:31 ./usr/lib/debug/.build-id/9f/bf1dbb535484d41e0253396161409ea85a6004.debug
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/debug/.build-id/e7/
-rw-r--r-- root/root 197832 2021-07-18 19:31 ./usr/lib/debug/.build-id/e7/81fbfa0bd6456452fe8340edd191af9a359a2a.debug
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/lib/debug/.build-id/f1/
-rw-r--r-- root/root 245976 2021-07-18 19:31 ./usr/lib/debug/.build-id/f1/a68879f1b47293a77ec53b87f18a0a63bb8f4e.debug
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-07-18 19:31 ./usr/share/doc/tabix-dbgsym -> tabix
tabix_1.9-12~deb10u1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 240808 bytes: control archive=1112 bytes.
972 bytes, 19 lines control
481 bytes, 8 lines md5sums
Package: tabix
Source: htslib
Version: 1.9-12~deb10u1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 800
Depends: libbz2-1.0, libc6 (>= 2.15), libcurl3-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), 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 2021-07-18 19:31 ./
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/bin/
-rwxr-xr-x root/root 83412 2021-07-18 19:31 ./usr/bin/bgzip
-rwxr-xr-x root/root 349660 2021-07-18 19:31 ./usr/bin/htsfile
-rwxr-xr-x root/root 349652 2021-07-18 19:31 ./usr/bin/tabix
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/doc/tabix/
-rw-r--r-- root/root 4453 2021-07-18 19:31 ./usr/share/doc/tabix/changelog.Debian.gz
-rw-r--r-- root/root 8097 2018-07-18 08:33 ./usr/share/doc/tabix/changelog.gz
-rw-r--r-- root/root 5762 2019-09-04 08:27 ./usr/share/doc/tabix/copyright
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/man/
drwxr-xr-x root/root 0 2021-07-18 19:31 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2021-07-18 19:31 ./usr/share/man/man1/bgzip.1.gz -> tabix.1.gz
-rw-r--r-- root/root 1700 2021-07-18 19:31 ./usr/share/man/man1/htsfile.1.gz
-rw-r--r-- root/root 2770 2021-07-18 19:31 ./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: 47496
Build-Time: 1563
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 234
Job: htslib_1.9-12~deb10u1
Machine Architecture: armhf
Package: htslib
Package-Time: 1845
Source-Version: 1.9-12~deb10u1
Space: 47496
Status: successful
Version: 1.9-12~deb10u1
--------------------------------------------------------------------------------
Finished at 2021-10-10T21:22:45Z
Build needed 00:30:45, 47496k disc space