htslib →
1.13+ds-2+b1 →
armhf → 2022-06-14 22:07:49
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| htslib 1.13+ds-2+b1 (armhf) Tue, 14 Jun 2022 21:23:55 +0000 |
+==============================================================================+
Package: htslib
Version: 1.13+ds-2+b1
Source Version: 1.13+ds-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-fbe21361-d4ea-4488-ba5b-d904ab9a9824' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.0 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.0 MB]
Fetched 27.0 MB in 29s (945 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| 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 1390 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main htslib 1.13+ds-2 (dsc) [2446 B]
Get:2 http://172.17.4.1/private bookworm-staging/main htslib 1.13+ds-2 (tar) [1370 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main htslib 1.13+ds-2 (diff) [17.5 kB]
Fetched 1390 kB in 0s (3807 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/htslib-DCqo18/htslib-1.13+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/htslib-DCqo18' 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-PNF2dB/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-PNF2dB/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-PNF2dB/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-PNF2dB/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-PNF2dB/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-PNF2dB/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-PNF2dB/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-PNF2dB/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2817 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 packages were automatically installed and are no longer required:
netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 72 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-PNF2dB/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 (22.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12621 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-compat (= 13), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0)
Filtered Build-Depends: debhelper-compat (= 13), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0)
dpkg-deb: building package 'sbuild-build-depends-htslib-dummy' in '/<<BUILDDIR>>/resolver-PNF2dB/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-PNF2dB/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-PNF2dB/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-PNF2dB/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-PNF2dB/apt_archive ./ Sources [556 B]
Get:5 copy:/<<BUILDDIR>>/resolver-PNF2dB/apt_archive ./ Packages [634 B]
Fetched 2523 B in 1s (3486 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 bsdextrautils bzip2 debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-1.0
libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl
libhtscodecs-dev libhtscodecs2 libicu71 liblzma-dev libmagic-mgc libmagic1
libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl-dev
libssl3 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
po-debconf zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc bzip2-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev
libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config
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
publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev
libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev
libdeflate0 libelf1 libfile-stripnondeterminism-perl libhtscodecs-dev
libhtscodecs2 libicu71 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl3
libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf
sbuild-build-depends-htslib-dummy zlib1g-dev
The following packages will be upgraded:
bzip2 libbz2-1.0 zlib1g
3 upgraded, 48 newly installed, 0 to remove and 69 not upgraded.
Need to get 26.6 MB of archives.
After this operation, 90.4 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-PNF2dB/apt_archive ./ sbuild-build-depends-htslib-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf zlib1g armhf 1:1.2.11.dfsg-4+b2 [84.5 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf bzip2 armhf 1.0.8-5+b2 [47.4 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libbz2-1.0 armhf 1.0.8-5+b2 [43.5 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38-4 [137 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-1 [33.7 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-1 [1362 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-6 [171 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-6 [510 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.7.1 [195 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-1 [175 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-6 [1214 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.7.1 [1071 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf dh-exec armhf 0.23.4+b1 [25.9 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.47.0-1+b1 [65.3 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libssl3 armhf 3.0.3-7 [1645 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.83.1-1 [313 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.83.1-1 [389 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.10-2 [55.4 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.10-2 [47.8 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.2.1-1 [52.7 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs-dev armhf 1.2.1-1 [2569 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2.1 [218 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libssl-dev armhf 3.0.3-7 [2122 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4+b2 [183 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 12621 files and directories currently installed.)
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Setting up zlib1g:armhf (1:1.2.11.dfsg-4+b2) ...
(Reading database ... 12622 files and directories currently installed.)
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Setting up libbz2-1.0:armhf (1.0.8-5+b2) ...
Selecting previously unselected package libuchardet0:armhf.
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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssl3:armhf.
Preparing to unpack .../36-libssl3_3.0.3-7_armhf.deb ...
Unpacking libssl3:armhf (3.0.3-7) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../37-libssh2-1_1.10.0-3+b1_armhf.deb ...
Unpacking libssh2-1:armhf (1.10.0-3+b1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../38-libcurl3-gnutls_7.83.1-1_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.83.1-1) ...
Selecting previously unselected package libcurl4-gnutls-dev:armhf.
Preparing to unpack .../39-libcurl4-gnutls-dev_7.83.1-1_armhf.deb ...
Unpacking libcurl4-gnutls-dev:armhf (7.83.1-1) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../40-libdeflate0_1.10-2_armhf.deb ...
Unpacking libdeflate0:armhf (1.10-2) ...
Selecting previously unselected package libdeflate-dev:armhf.
Preparing to unpack .../41-libdeflate-dev_1.10-2_armhf.deb ...
Unpacking libdeflate-dev:armhf (1.10-2) ...
Selecting previously unselected package libhtscodecs2:armhf.
Preparing to unpack .../42-libhtscodecs2_1.2.1-1_armhf.deb ...
Unpacking libhtscodecs2:armhf (1.2.1-1) ...
Selecting previously unselected package libhtscodecs-dev:armhf.
Preparing to unpack .../43-libhtscodecs-dev_1.2.1-1_armhf.deb ...
Unpacking libhtscodecs-dev:armhf (1.2.1-1) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../44-liblzma-dev_5.2.5-2.1_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.5-2.1) ...
Selecting previously unselected package libssl-dev:armhf.
Preparing to unpack .../45-libssl-dev_3.0.3-7_armhf.deb ...
Unpacking libssl-dev:armhf (3.0.3-7) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../46-zlib1g-dev_1%3a1.2.11.dfsg-4+b2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-4+b2) ...
Selecting previously unselected package sbuild-build-depends-htslib-dummy.
Preparing to unpack .../47-sbuild-build-depends-htslib-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Setting up libhtscodecs2:armhf (1.2.1-1) ...
Setting up libpipeline1:armhf (1.5.6-1) ...
Setting up libicu71:armhf (71.1-3) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.38-4) ...
Setting up libmagic-mgc (1:5.41-4) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.7.1) ...
Setting up libbrotli1:armhf (1.0.9-2+b2) ...
Setting up libssl3:armhf (3.0.3-7) ...
Setting up libnghttp2-14:armhf (1.47.0-1+b1) ...
Setting up libmagic1:armhf (1:5.41-4) ...
Setting up libdeflate0:armhf (1.10-2) ...
Setting up gettext-base (0.21-6) ...
Setting up file (1:5.41-4) ...
Setting up bzip2 (1.0.8-5+b2) ...
Setting up libhtscodecs-dev:armhf (1.2.1-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libsigsegv2:armhf (2.14-1) ...
Setting up libssl-dev:armhf (3.0.3-7) ...
Setting up autopoint (0.21-6) ...
Setting up liblzma-dev:armhf (5.2.5-2.1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-4+b2) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.10.0-3+b1) ...
Setting up libdeflate-dev:armhf (1.10-2) ...
Setting up libelf1:armhf (0.187-1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1) ...
Setting up libbz2-dev:armhf (1.0.8-5+b2) ...
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up gettext (0.21-6) ...
Setting up libtool (2.4.7-4) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.83.1-1) ...
Setting up libcurl4-gnutls-dev:armhf (7.83.1-1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-8) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.10.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.7.1) ...
Setting up dh-exec (0.23.4+b1) ...
Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.33-7+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.38-3+rpi1 dpkg-dev_1.21.7+rpi1 g++-11_11.2.0-20+rpi1 gcc-11_11.2.0-20+rpi1 libc6-dev_2.33-7+rpi1 libstdc++-11-dev_11.2.0-20+rpi1 libstdc++6_12-20220319-1+rpi1 linux-libc-dev_5.16.18-1+rpi1
Package versions: adduser_3.121 apt_2.4.5 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.5.52 bash_5.1-6 binutils_2.38-3+rpi1 binutils-arm-linux-gnueabihf_2.38-3+rpi1 binutils-common_2.38-3+rpi1 bsdextrautils_2.38-4 bsdutils_1:2.38-4 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-20+rpi1 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.7.1 debianutils_5.7-0.1 dh-autoreconf_20 dh-exec_0.23.4+b1 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-3+b1 dpkg_1.21.7+rpi1 dpkg-dev_1.21.7+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.28-1 file_1:5.41-4 findutils_4.9.0-2 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-20+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-20+rpi1 gcc-11-base_11.2.0-20+rpi1 gcc-12-base_12-20220319-1+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-6 gettext-base_0.21-6 gnupg_2.2.27-3 gnupg-l10n_2.2.27-3 gnupg-utils_2.2.27-3+b1 gpg_2.2.27-3+b1 gpg-agent_2.2.27-3+b1 gpg-wks-client_2.2.27-3+b1 gpg-wks-server_2.2.27-3+b1 gpgconf_2.2.27-3+b1 gpgsm_2.2.27-3+b1 gpgv_2.2.27-3+b1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 init-system-helpers_1.62 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.4.5 libarchive-zip-perl_1.68-1 libasan6_11.2.0-20+rpi1 libassuan0_2.5.5-1 libatomic1_12-20220319-1+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbinutils_2.38-3+rpi1 libblkid1_2.38-4 libbrotli1_1.0.9-2+b2 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.33-7+rpi1 libc-dev-bin_2.33-7+rpi1 libc6_2.33-7+rpi1 libc6-dev_2.33-7+rpi1 libcap-ng0_0.7.9-2.2+b2 libcap2_1:2.44-1 libcc1-0_12-20220319-1+rpi1 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.38-3+rpi1 libctf0_2.38-3+rpi1 libcurl3-gnutls_7.83.1-1 libcurl4-gnutls-dev_7.83.1-1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.262 libdebhelper-perl_13.7.1 libdeflate-dev_1.10-2 libdeflate0_1.10-2 libdpkg-perl_1.21.7+rpi1 libelf1_0.187-1 libext2fs2_1.46.5-2 libfakeroot_1.28-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-11-dev_11.2.0-20+rpi1 libgcc-s1_12-20220319-1+rpi1 libgcrypt20_1.10.1-2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.4-2 libgomp1_12-20220319-1+rpi1 libgpg-error0_1.43-3 libgssapi-krb5-2_1.19.2-2+b2 libhogweed6_3.7.3-1 libhtscodecs-dev_1.2.1-1 libhtscodecs2_1.2.1-1 libicu71_71.1-3 libidn2-0_2.3.2-2 libisl23_0.24-2 libk5crypto3_1.19.2-2+b2 libkeyutils1_1.6.1-3+rpi1 libkrb5-3_1.19.2-2+b2 libkrb5support0_1.19.2-2+b2 libksba8_1.6.0-2 libldap-2.5-0_2.5.11+dfsg-1+rpi1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2.1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38-4 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libncursesw6_6.3-2 libnettle8_3.7.3-1 libnghttp2-14_1.47.0-1+b1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-modules_1.4.0-11 libpam-modules-bin_1.4.0-11 libpam-runtime_1.4.0-11 libpam0g_1.4.0-11 libpcre2-8-0_10.39-4 libpcre3_2:8.39-14 libperl5.34_5.34.0-4 libpipeline1_1.5.6-1 libpsl5_0.21.0-1.2 libreadline8_8.1.2-1.2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-4 libsasl2-modules-db_2.1.28+dfsg-4 libseccomp2_2.5.3-2+rpi1+b1 libselinux1_3.3-1+b1 libsemanage-common_3.3-1 libsemanage2_3.3-1+b1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.14-1 libsmartcols1_2.38-4 libsqlite3-0_3.38.2-1 libss2_1.46.5-2 libssh2-1_1.10.0-3+b1 libssl-dev_3.0.3-7 libssl1.1_1.1.1n-1 libssl3_3.0.3-7 libstdc++-11-dev_11.2.0-20+rpi1 libstdc++6_12-20220319-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_250.4-1+rpi1 libtasn1-6_4.18.0-4 libtinfo6_6.3-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.7-4 libubsan1_12-20220319-1+rpi1 libuchardet0_0.0.7-1 libudev1_250.4-1+rpi1 libunistring2_1.0-1 libuuid1_2.38-4 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.16.18-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.2-1 mawk_1.3.4.20200120-3 mount_2.38-4 ncurses-base_6.3-2 ncurses-bin_6.3-2 netbase_6.3 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-4 perl-base_5.34.0-4 perl-modules-5.34_5.34.0-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.03-1 tar_1.34+dfsg-1 tzdata_2022a-1 util-linux_2.37.3-1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4+b2 zlib1g-dev_1:1.2.11.dfsg-4+b2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.VQhc6Z44/trustedkeys.kbx': General error
gpgv: Signature made Fri Aug 27 20:28:31 2021 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./htslib_1.13+ds-2.dsc
dpkg-source: info: extracting htslib in /<<BUILDDIR>>/htslib-1.13+ds
dpkg-source: info: unpacking htslib_1.13+ds.orig.tar.bz2
dpkg-source: info: unpacking htslib_1.13+ds-2.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
dpkg-source: info: applying cram_to_bam_export.patch
dpkg-source: info: applying disable_plugin_loading_test.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.13+ds-2+b1
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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-fbe21361-d4ea-4488-ba5b-d904ab9a9824
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 1.13+ds-2+b1
dpkg-buildpackage: info: source distribution bookworm-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from htslib-1.13+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_auto_clean
install -d /<<BUILDDIR>>/htslib-1.13\+ds/debian/.debhelper/generated/_source/home
make -j4 distclean
make[2]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -f test/*.tmp test/*.tmp.* test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL* header-exports.txt shlib-exports-so.txt
rm -f libhts.so libhts.so.*
rm -rf htscodecs/tests/test.out
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM config_vars.h version.h
rm -f htscodecs/htscodecs/*.o htscodecs/htscodecs/*.pico
rm -f hts-object-files
rm -f htscodecs/tests/*.o
rm -f libhts.a bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/plugins-dlhts test/sam test/test_bgzf test/test_expr test/test_kfunc test/test_kstring test/test_realn test/test-regidx test/test_str2int test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/test_introspection test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7
rm -f htscodecs/tests/rans4x8 htscodecs/tests/rans4x16pr htscodecs/tests/arith_dynamic htscodecs/tests/tokenise_name3 htscodecs/tests/fqzcomp_qual htscodecs/tests/varint
rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk htscodecs.mk
rm -rf autom4te.cache
make[2]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -rf test_backup/
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/libhts3.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files
rm -fr -- debian/libhts3/ debian/tmp/ debian/libhts-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 binary-arch
dh binary-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 '/<<BUILDDIR>>/htslib-1.13+ds'
# create clean copy of test dir
cp -a test test_backup
# to help with cross building, otherwise MMAP might get turned off
export ac_cv_func_mmap_fixed_mapped=yes && autoconf && \
dh_auto_configure -- --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir='/htslib' --with-external-htscodecs --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:'
install -d /<<BUILDDIR>>/htslib-1.13\+ds/debian/.debhelper/generated/_source/home
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir=/htslib --with-external-htscodecs --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... 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 pkg-config... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking shared library type for unknown-Linux... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... (cached) yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking for srand48_deterministic... no
checking for gcc options needed to detect all undeclared functions... none needed
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing dlsym... -ldl
checking whether the compiler accepts -rdynamic... 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 htscodecs/rANS_static4x16.h... yes
checking for rans_compress_bound_4x16 in -lhtscodecs... yes
checking for libdeflate.h... yes
checking for libdeflate_deflate_compress in -ldeflate... yes
checking for curl/curl.h... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
checking for library containing regcomp... none required
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
config.status: linking htscodecs_external.mk to htscodecs.mk
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_auto_build-arch
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_auto_build -- \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
PACKAGE_VERSION="1.13+ds" \
libdir=/usr/lib/arm-linux-gnueabihf
make -j4 "CFLAGS=-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden" PACKAGE_VERSION=1.13\+ds libdir=/usr/lib/arm-linux-gnueabihf
make[2]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.13+ds"' > version.h
echo '#define HTS_CC "gcc"' > config_vars.h
echo '#define HTS_CPPFLAGS "-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2"' >> config_vars.h
echo '#define HTS_CFLAGS "-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LDFLAGS "-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LIBS "-ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl "' >> config_vars.h
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -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 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:\" -c -o plugin.o plugin.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_expr.pico hts_expr.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -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 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:\" -fPIC -c -o plugin.pico plugin.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/plugins-dlhts.o test/plugins-dlhts.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_expr.o test/test_expr.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kfunc.o test/test_kfunc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kstring.o test/test_kstring.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_str2int.o test/test_str2int.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_index.o test/test_index.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -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 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -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 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -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 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -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 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_introspection.o test/test_introspection.c
sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk
sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
gcc -shared -Wl,-soname,libhts.so.3 -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.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_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico plugin.pico -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/hts_endian test/hts_endian.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl
ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.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_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o plugin.o
ranlib libhts.a
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o bgzip bgzip.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o htsfile htsfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o tabix tabix.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/sam test/sam.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_expr test/test_expr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_kfunc test/test_kfunc.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
ln -sf libhts.so libhts.so.3
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lcurl -lpthread
gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lcrypto -lpthread
gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o hfile_s3_write.so hfile_s3_write.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lcrypto -lcurl -lpthread
make[2]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_auto_test-arch
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_auto_test -- \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
PACKAGE_VERSION="1.13+ds" \
libdir=/usr/lib/arm-linux-gnueabihf \
|| \
if find . -name "FAIL*" > /dev/null ; then \
for file in $(find . -name "FAIL*"); do echo ${file}; cat ${file}; done && false ; \
fi
make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 "CFLAGS=-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden" PACKAGE_VERSION=1.13\+ds libdir=/usr/lib/arm-linux-gnueabihf
make[2]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
test/hts_endian
test/test_expr
test/test_kfunc
test/test_kstring
test/test_str2int
test/fieldarith test/fieldarith.sam
test/hfile
HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so
HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so
test/test_bgzf test/bgziptest.txt
test/test-parse-reg -t test/colons.bam
Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead
Expected error: [E::hts_parse_region] Mismatching braces in "{chr1"
Expected error: [E::hts_parse_region] Unexpected string "x" after region
Expected error: [E::hts_parse_region] Unexpected string "y" after region
Expected error: [E::hts_parse_region] Unexpected string "chr3" after region
cd test/sam_filter && ./filter.sh filter.tst
Testing sam_filter...
PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam
PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam
PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam
PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam
PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam
PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam
PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam
PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam |egrep -cv '^@'
PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam |egrep -cv '^@'
PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam |egrep -cv '^@'
PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | egrep -cv '^@'
PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | egrep -cv '^@'
PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | egrep -cv '^@'
PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | egrep -cv '^@'
Expected passes: 14
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
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
PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005
Expected passes: 14
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
cd test/mpileup && ./test-pileup.sh mpileup.tst
Testing (m)pileup...
PASS : $pileup mp_D.sam
PASS : $pileup -m mp_D.sam
PASS : $pileup mp_DI.sam
PASS : $pileup -m mp_DI.sam
PASS : $pileup mp_I.sam
PASS : $pileup -m mp_I.sam
PASS : $pileup mp_P.sam
PASS : $pileup -m mp_P.sam
PASS : $pileup mp_ID.sam
PASS : $pileup -m mp_ID.sam
PASS : $pileup mp_N.sam
PASS : $pileup -m mp_N.sam
PASS : $pileup mp_N2.sam
PASS : $pileup -m mp_N2.sam
PASS : $pileup c1#pad1.sam
PASS : $pileup -m c1#pad1.sam
PASS : $pileup c1#pad2.sam
PASS : $pileup -m c1#pad2.sam
PASS : $pileup c1#pad3.sam
PASS : $pileup -m c1#pad3.sam
PASS : $pileup -m small.bam
Expected passes: 21
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
cd test/fastq && ./test-fastq.sh
Testing fastq support
PASS : $tview minimal.fq
PASS : $tview minimal.fa
PASS : $tview multiline.fq
PASS : $tview multiline.fa
PASS : $tview single.fq
PASS : $tview single.fa
PASS : $tview -i fastq_aux single.fq
PASS : $tview -i fastq_aux single.fa
PASS : $tview interleaved.fq
PASS : $tview interleaved.fa
PASS : $tview -i fastq_aux interleaved.fq
PASS : $tview -i fastq_aux interleaved.fa
PASS : $tview -i fastq_casava interleaved_casava.fq
PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq
PASS : $tview -i fastq_casava interleaved_casava.fa
PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa
PASS : $tview -i fastq_casava filter_casava.fq
PASS : $tview -i fastq_casava filter_casava.fa
PASS : $tview -i fastq_aux r1.fq
PASS : $tview -i fastq_aux r2.fq
PASS : $tview -i fastq_aux r1.fa
PASS : $tview -i fastq_aux r2.fa
PASS : $tview -f minimal.sam
PASS : $tview -F minimal.sam
PASS : $tview -f -o fastq_aux single_aux.sam
PASS : $tview -F -o fastq_aux single_aux.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam
PASS : $tview -f -o fastq_casava inter_casava.sam
PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam
PASS : $tview -F -o fastq_casava inter_casava.sam
PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam
PASS : $tview -f -o fastq_casava filter_casava.sam
PASS : $tview -F -o fastq_casava filter_casava.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam
Expected passes: 38
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:-}
bgzip round-trip no threads: .. ok
bgzip -b no threads: .. ok
bgzip -b -I no threads: .. ok
bgzip round-trip 4 threads: .. ok
bgzip -b 4 threads: .. ok
bgzip -b -I 4 threads: .. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -b -m 14 -x /tmp/S6aT5QQoXS/index.bam.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/S6aT5QQoXS/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/S6aT5QQoXS/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -b -m 0 -x /tmp/S6aT5QQoXS/index.bam.bai /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/S6aT5QQoXS/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -b /tmp/S6aT5QQoXS/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -z -m 14 -x /tmp/S6aT5QQoXS/index.sam.gz.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -z -m 0 -x /tmp/S6aT5QQoXS/index.sam.gz.bai /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -b /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -z -m 14 -x /tmp/S6aT5QQoXS/index.sam.gz.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index_dos.sam > /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -z -m 0 -x /tmp/S6aT5QQoXS/index.sam.gz.bai /<<BUILDDIR>>/htslib-1.13+ds/test/index_dos.sam > /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -b /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -C -x /tmp/S6aT5QQoXS/index.cram.crai /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/S6aT5QQoXS/index.cram
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index /tmp/S6aT5QQoXS/index.cram
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -b -m 14 -x /tmp/S6aT5QQoXS/index.bcf.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.vcf > /tmp/S6aT5QQoXS/index.bcf
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/S6aT5QQoXS/index.bcf
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -z -m 14 -x /tmp/S6aT5QQoXS/index.vcf.gz.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.vcf > /tmp/S6aT5QQoXS/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/S6aT5QQoXS/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -z -m 0 -x /tmp/S6aT5QQoXS/index.vcf.gz.tbi /<<BUILDDIR>>/htslib-1.13+ds/test/index.vcf > /tmp/S6aT5QQoXS/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -t /tmp/S6aT5QQoXS/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/tabix /tmp/S6aT5QQoXS/index.vcf.gz##idx##/tmp/S6aT5QQoXS/index.vcf.gz.tbi 1:10000060-10000060
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/S6aT5QQoXS/index.bam.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/S6aT5QQoXS/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/S6aT5QQoXS/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -b -m 0 -x /tmp/S6aT5QQoXS/index.bam.bai /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/S6aT5QQoXS/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -b /tmp/S6aT5QQoXS/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/S6aT5QQoXS/index.sam.gz.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/S6aT5QQoXS/index.sam.gz.bai /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -b /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/S6aT5QQoXS/index.sam.gz.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index_dos.sam > /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/S6aT5QQoXS/index.sam.gz.bai /<<BUILDDIR>>/htslib-1.13+ds/test/index_dos.sam > /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -b /tmp/S6aT5QQoXS/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -C -x /tmp/S6aT5QQoXS/index.cram.crai /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/S6aT5QQoXS/index.cram
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index /tmp/S6aT5QQoXS/index.cram
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/S6aT5QQoXS/index.bcf.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.vcf > /tmp/S6aT5QQoXS/index.bcf
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/S6aT5QQoXS/index.bcf
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/S6aT5QQoXS/index.vcf.gz.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.vcf > /tmp/S6aT5QQoXS/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/S6aT5QQoXS/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/S6aT5QQoXS/index.vcf.gz.tbi /<<BUILDDIR>>/htslib-1.13+ds/test/index.vcf > /tmp/S6aT5QQoXS/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -t /tmp/S6aT5QQoXS/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/tabix /tmp/S6aT5QQoXS/index.vcf.gz##idx##/tmp/S6aT5QQoXS/index.vcf.gz.tbi 1:10000060-10000060
.. ok
test_view testing multi-ref CRAM modes:
./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
.. ok
test_view testing multi-ref CRAM modes:
./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
.. ok
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 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o fast auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
./test_view -t auxf.fa -C -o VERSION=3.1 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t auxf.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o fast auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
./test_view -t auxf.fa -C -o VERSION=4.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t auxf.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t c2.fa -S -l7 -C -o VERSION=3.1 -o fast c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
./test_view -t c2.fa -C -o VERSION=3.1 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c2.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
./test_view -t c2.fa -C -o VERSION=4.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c2.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#1.tmp.bam > ce#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#1.tmp.cram > ce#1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#1.tmp.cram > ce#1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#2.tmp.bam > ce#2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#2.tmp.cram > ce#2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#2.tmp.cram > ce#2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#5.tmp.bam > ce#5.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#5.tmp.cram > ce#5.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#5.tmp.cram > ce#5.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t md.fa -S -l7 -C -o VERSION=3.1 -o fast md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 md#1.tmp.bam > md#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 md#1.tmp.cram > md#1.tmp.cram.cram
./test_view -t md.fa -C -o VERSION=3.1 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t md.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 md#1.tmp.bam > md#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 md#1.tmp.cram > md#1.tmp.cram.cram
./test_view -t md.fa -C -o VERSION=4.0 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t md.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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#MD.sam, ref xx.fa:
./test_view -S -b xx#MD.sam > xx#MD.tmp.bam
./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam
./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
./test_view -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD.sam > xx#MD.tmp.cram
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
./test_view -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#MD.tmp.cram > xx#MD.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
./test_view xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o normal xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o small xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.1 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram > xx#MD.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=4.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram > xx#MD.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
.. ok
test_view testing xx#MD2.sam, ref xx.fa:
./test_view -S -b xx#MD2.sam > xx#MD2.tmp.bam
./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam
./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
./test_view -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD2.sam > xx#MD2.tmp.cram
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
./test_view -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
./test_view xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o normal xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o small xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=4.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
.. ok
test_view testing region queries:
./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
.. ok
test_view testing BAM files with absent @SQ lines:
./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam
./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam
./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I
./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam
.. ok
test_view testing large (> 2Gbases) positions:
./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam
./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz
./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_
test_view:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c longrefs/longref.tmp.sam.gz
.. ok
./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003
./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam
./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110
./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam
.. ok
test_view testing auxf#values.sam, ref auxf.fa:
./test_view -@4 -S -b auxf#values.sam > auxf#values.tmp.bam
./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
./test_view -@4 -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 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o fast auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
./test_view -@4 -t auxf.fa -C -o VERSION=3.1 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t auxf.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o fast auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
./test_view -@4 -t auxf.fa -C -o VERSION=4.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t auxf.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t c2.fa -S -l7 -C -o VERSION=3.1 -o fast c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
./test_view -@4 -t c2.fa -C -o VERSION=3.1 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c2.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
./test_view -@4 -t c2.fa -C -o VERSION=4.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c2.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#1.tmp.bam > ce#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#1.tmp.cram > ce#1.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#1.tmp.cram > ce#1.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#2.tmp.bam > ce#2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#2.tmp.cram > ce#2.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#2.tmp.cram > ce#2.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#5.tmp.bam > ce#5.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#5.tmp.cram > ce#5.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#5.tmp.cram > ce#5.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t md.fa -S -l7 -C -o VERSION=3.1 -o fast md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 md#1.tmp.bam > md#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 md#1.tmp.cram > md#1.tmp.cram.cram
./test_view -@4 -t md.fa -C -o VERSION=3.1 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t md.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 md#1.tmp.bam > md#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 md#1.tmp.cram > md#1.tmp.cram.cram
./test_view -@4 -t md.fa -C -o VERSION=4.0 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t md.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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#MD.sam, ref xx.fa:
./test_view -@4 -S -b xx#MD.sam > xx#MD.tmp.bam
./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam
./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
./test_view -@4 -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view -@4 xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD.sam > xx#MD.tmp.cram
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
./test_view -@4 -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view -@4 xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD.tmp.cram > xx#MD.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
./test_view -@4 xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o normal xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o small xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view -@4 xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram > xx#MD.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view -@4 xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram > xx#MD.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
.. ok
test_view testing xx#MD2.sam, ref xx.fa:
./test_view -@4 -S -b xx#MD2.sam > xx#MD2.tmp.bam
./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam
./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
./test_view -@4 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD2.sam > xx#MD2.tmp.cram
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
./test_view -@4 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
./test_view -@4 xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o normal xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o small xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o normal xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o small xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=4.0 -o archive xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=4.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 testing region queries:
./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
.. ok
test_view testing BAM files with absent @SQ lines:
./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam
./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam
./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I
./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam
.. ok
test_view testing large (> 2Gbases) positions:
./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam
./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz
./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_
test_view:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c longrefs/longref.tmp.sam.gz
.. ok
./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003
./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam
./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110
./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam
.. ok
test_MD testing xx#MD.sam, ref xx.fa:
./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_
Checking for MD/NM in xx#MD.sam
./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_
.. ok
test_MD testing xx#MD2.sam, ref xx.fa:
./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_
.. ok
test_vcf_api:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-vcf-api /tmp/S6aT5QQoXS/test-vcf-api.bcf
[W::bcf_record_check] Bad BCF record at 1:1: No REF allele
[E::bcf_index_build3] TBI indices for BCF files are not supported
[E::idx_find_and_load] Could not retrieve index file for '/tmp/S6aT5QQoXS/test-vcf-api.bcf'
.. ok
test_bcf2vcf:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view /<<BUILDDIR>>/htslib-1.13+ds/test/tabix/vcf_file.bcf
.. ok
test_vcf_sweep:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-vcf-sweep /tmp/S6aT5QQoXS/test-vcf-api.bcf
.. ok
test_vcf_various:
/<<BUILDDIR>>/htslib-1.13+ds/htsfile -ch /<<BUILDDIR>>/htslib-1.13+ds/test/test-vcf-hdr-in.vcf
.. ok
test_vcf_various:
/<<BUILDDIR>>/htslib-1.13+ds/htsfile -c /<<BUILDDIR>>/htslib-1.13+ds/test/formatcols.vcf
.. ok
test_vcf_various:
/<<BUILDDIR>>/htslib-1.13+ds/htsfile -c /<<BUILDDIR>>/htslib-1.13+ds/test/noroundtrip.vcf
.. ok
test_vcf_various:
/<<BUILDDIR>>/htslib-1.13+ds/htsfile -c /<<BUILDDIR>>/htslib-1.13+ds/test/formatmissing.vcf
.. ok
test_vcf_various:
/<<BUILDDIR>>/htslib-1.13+ds/htsfile -c /<<BUILDDIR>>/htslib-1.13+ds/test/vcf_meta_meta.vcf
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/S6aT5QQoXS -s 1491990251
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/S6aT5QQoXS -s 1146932001
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/S6aT5QQoXS -s 1449505942
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/S6aT5QQoXS -s 1647960599
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/S6aT5QQoXS -s 6816764
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/S6aT5QQoXS -s 485690947
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/S6aT5QQoXS -s 1126673806
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/S6aT5QQoXS -s 201131661
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/S6aT5QQoXS -s 1289222026
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/S6aT5QQoXS -s 1137608279
.. ok
test_command:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-translate -
.. ok
test_convert_padded_header:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -t ce.fa -C /tmp/S6aT5QQoXS/headernul0.bam
.. ok
test_convert_padded_header:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -t ce.fa -C /tmp/S6aT5QQoXS/headernul1.bam
.. ok
test_convert_padded_header:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -t ce.fa -C /tmp/S6aT5QQoXS/headernul678.bam
.. ok
test_rebgzip: Alternate zlib/deflate library detected
test_rebgzip:
/<<BUILDDIR>>/htslib-1.13+ds/bgzip -I /<<BUILDDIR>>/htslib-1.13+ds/test/bgziptest.txt.tmp.gz.gzi -c -g /<<BUILDDIR>>/htslib-1.13+ds/test/bgziptest.txt
.. ok
test-logging:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-logging.pl
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn01.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn01.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -a -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn01.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn01.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -a -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -e -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn01.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn01.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -e -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -r -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn02-r.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -a -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn02_exp.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn02_exp-a.sam -o -
.. ok
Number of tests:
total .. 163
passed .. 163
failed .. 0
make[2]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -fr -- /tmp/dh-xdg-rundir-a82KbroD
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
create-stamp debian/debhelper-build-stamp
dh_prep -a
rm -f -- debian/libhts3.substvars debian/libhts-dev.substvars debian/tabix.substvars
rm -fr -- debian/.debhelper/generated/libhts3/ debian/libhts3/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/tabix/ debian/tabix/
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \
rm /<<BUILDDIR>>/htslib-1.13+ds/test/${binary} ; \
done
dh_auto_install -- prefix=/usr \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
PACKAGE_VERSION="1.13+ds" \
libdir=/usr/lib/arm-linux-gnueabihf
install -d /<<BUILDDIR>>/htslib-1.13\+ds/debian/tmp
make -j4 install DESTDIR=/<<BUILDDIR>>/htslib-1.13\+ds/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr "CFLAGS=-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden" PACKAGE_VERSION=1.13\+ds libdir=/usr/lib/arm-linux-gnueabihf
make[2]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
mkdir -p -m 755 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/bin /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/include /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/include/htslib /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/share/man/man1 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/share/man/man5 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/share/man/man7 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig
if test -n "/htslib"; then mkdir -p -m 755 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/htslib; fi
install -p -m 644 libhts.so /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.13+ds
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/arm-linux-gnueabihf#g;s#@-PACKAGE_VERSION@#1.13+ds#g' htslib.pc.tmp > /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
chmod 644 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
ln -sf libhts.so.1.13+ds /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so
ln -sf libhts.so.1.13+ds /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3
install -p bgzip htsfile tabix /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/bin
if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/htslib; fi
install -p -m 644 htslib/*.h /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/include/htslib
install -p -m 644 libhts.a /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a
install -p -m 644 bgzip.1 htsfile.1 tabix.1 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/share/man/man5
install -p -m 644 htslib-s3-plugin.7 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/share/man/man7
make[2]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
# 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 '/<<BUILDDIR>>/htslib-1.13+ds'
dh_install -a
install -d debian/libhts3/usr/lib/arm-linux-gnueabihf
cp --reflink=auto -a ./debian/tmp/htslib debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3 debian/libhts3/usr/lib/arm-linux-gnueabihf/
install -d debian/libhts3/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/libhts3/usr/share/man/man5/
install -d debian/.debhelper/generated/libhts3
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/.debhelper/generated/libhts-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
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_installdocs
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_installdocs
install -d debian/libhts3/usr/share/doc/libhts3
install -p -m0644 debian/copyright debian/libhts3/usr/share/doc/libhts3/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
cp --reflink=auto -a ./README.large_positions.md debian/libhts-dev/usr/share/doc/libhts-dev
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
# Fix Perl interpreter path
for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
grep: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so: No such file or directory
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_installchangelogs NEWS
install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog
install -p -m0644 NEWS debian/libhts3/usr/share/doc/libhts3/changelog
install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_installman -a
install -d debian/libhts3/usr/share/man/man7/
install -p -m0644 ./htslib-s3-plugin.7 debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7
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
install -p -m0644 ./bgzip.1 debian/tabix/usr/share/man/man1/bgzip.1
man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man5/faidx.5 debian/libhts3/usr/share/man/man5/sam.5
man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man5/vcf.5 debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7
man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1
man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/tabix.1
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/libhts3/usr/share/man/man5/vcf.5.dh-new debian/libhts3/usr/share/man/man5/vcf.5
mv debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7
chmod 0644 -- debian/libhts3/usr/share/man/man5/vcf.5 debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7
mv debian/libhts3/usr/share/man/man5/faidx.5.dh-new debian/libhts3/usr/share/man/man5/faidx.5
mv debian/libhts3/usr/share/man/man5/sam.5.dh-new debian/libhts3/usr/share/man/man5/sam.5
chmod 0644 -- debian/libhts3/usr/share/man/man5/faidx.5 debian/libhts3/usr/share/man/man5/sam.5
mv debian/tabix/usr/share/man/man1/bgzip.1.dh-new debian/tabix/usr/share/man/man1/bgzip.1
mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1
chmod 0644 -- debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1
dh_perl -a
dh_link -a
rm -f debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.3
ln -s libhts.so.1.13\+ds debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.3
rm -f debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so
ln -s libhts.so.1.13\+ds 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/libhts3
cd debian/libhts-dev
cd debian/tabix
chmod a-x usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian usr/share/doc/libhts-dev/changelog.Debian.armhf
chmod a-x usr/share/doc/libhts3/changelog usr/share/doc/libhts3/changelog.Debian usr/share/doc/libhts3/changelog.Debian.armhf usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7
chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/doc/tabix/changelog.Debian.armhf usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1
gzip -9nf usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian usr/share/doc/libhts-dev/changelog.Debian.armhf
gzip -9nf usr/share/doc/libhts3/changelog usr/share/doc/libhts3/changelog.Debian usr/share/doc/libhts3/changelog.Debian.armhf usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7
gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/doc/tabix/changelog.Debian.armhf usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1
cd '/<<BUILDDIR>>/htslib-1.13+ds'
cd '/<<BUILDDIR>>/htslib-1.13+ds'
cd '/<<BUILDDIR>>/htslib-1.13+ds'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_fixperms
find debian/libhts3 ! -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/tabix ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
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/libhts3/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts3/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/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/libhts3/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/libhts-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts3/usr/share/man -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/libhts3 -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 -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
find debian/libhts3/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
find debian -name simple_test_driver.sh -exec chmod +x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_missing
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
# FIXME: No idea why these files are remaining in debian/tmp
rm -rf debian/tmp/usr/bin debian/tmp/usr/share/man
dh_missing
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_dwz -a
install -d debian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf
dwz -mdebian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug -- debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds
install -d debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf
dwz -mdebian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix
dwz: debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13+ds: DWARF compression not beneficial - old size 840219 new size 853277
objcopy --compress-debug-sections debian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug
objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_strip
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
# This is apparently important for the interpretation by ldc2 in sambamba
dh_strip -Xlibhts.a
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/36
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/36/63bf2081ff6fbf36141e4e81f2eaea3eebb13d.debug
install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/8c
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/8c/7755698ba53face9b33921b260328be54de611.debug
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/36/63bf2081ff6fbf36141e4e81f2eaea3eebb13d.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/36/63bf2081ff6fbf36141e4e81f2eaea3eebb13d.debug debian/tabix/usr/bin/bgzip
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/89
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/89/29b18bf9410f2033bb8685a532aec71352ea6a.debug
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/89/29b18bf9410f2033bb8685a532aec71352ea6a.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/89/29b18bf9410f2033bb8685a532aec71352ea6a.debug debian/tabix/usr/bin/htsfile
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/78
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/78/b493b45c540d2e60d1646ca8a8d07b83ba80b4.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/8c/7755698ba53face9b33921b260328be54de611.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/8c/7755698ba53face9b33921b260328be54de611.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds
install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/46
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/46/b913bc733c46bf5c9e3e3500a7066d7b1946a5.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/46/b913bc733c46bf5c9e3e3500a7066d7b1946a5.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/46/b913bc733c46bf5c9e3e3500a7066d7b1946a5.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so
install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/17
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/17/e744e932dc2f7a410d16cfd635497d26e814fa.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/17/e744e932dc2f7a410d16cfd635497d26e814fa.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/17/e744e932dc2f7a410d16cfd635497d26e814fa.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so
install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/00
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/00/463a9088228d34203fdacfa2e18408e45c8c5d.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/00/463a9088228d34203fdacfa2e18408e45c8c5d.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/00/463a9088228d34203fdacfa2e18408e45c8c5d.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so
install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/07
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/07/df06dc1dbd956a7f10dd1cff1fc0639916c49d.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/07/df06dc1dbd956a7f10dd1cff1fc0639916c49d.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/07/df06dc1dbd956a7f10dd1cff1fc0639916c49d.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so
install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/libhts3/usr/lib/debug/.dwz
rmdir -p --ignore-fail-on-non-empty debian/libhts3/usr/lib/debug
install -d debian/.debhelper/libhts3/dbgsym-root/usr/share/doc
ln -s libhts3 debian/.debhelper/libhts3/dbgsym-root/usr/share/doc/libhts3-dbgsym
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/78/b493b45c540d2e60d1646ca8a8d07b83ba80b4.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/78/b493b45c540d2e60d1646ca8a8d07b83ba80b4.debug debian/tabix/usr/bin/tabix
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/tabix/usr/lib/debug/.dwz
rmdir -p --ignore-fail-on-non-empty debian/tabix/usr/lib/debug
install -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc
ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_makeshlibs -a
rm -f debian/libhts3/DEBIAN/shlibs
install -d debian/libhts3/DEBIAN
echo "libhts 3 libhts3 (>= 1.13+ds)" >> debian/libhts3/DEBIAN/shlibs
chmod 0644 -- debian/libhts3/DEBIAN/shlibs
dpkg-gensymbols -plibhts3 -Idebian/libhts3.symbols -Pdebian/libhts3 -edebian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds
mv debian/.debhelper/generated/libhts3/triggers.new debian/.debhelper/generated/libhts3/triggers
rm -f debian/libhts-dev/DEBIAN/shlibs
rm -f debian/tabix/DEBIAN/shlibs
dh_shlibdeps -a
dpkg-shlibdeps -Tdebian/libhts3.substvars debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so
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/tabix debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/bgzip were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
install -p -m0644 debian/.debhelper/generated/libhts3/triggers debian/libhts3/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/libhts3.substvars
echo misc:Pre-Depends= >> debian/libhts3.substvars
install -d debian/.debhelper/libhts3/dbgsym-root/DEBIAN
dpkg-gencontrol -plibhts3 -ldebian/changelog -Tdebian/libhts3.substvars -Pdebian/.debhelper/libhts3/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=libhts3-dbgsym "-DDepends=libhts3 (= \${binary:Version})" "-DDescription=debug symbols for libhts3" "-DBuild-Ids=00463a9088228d34203fdacfa2e18408e45c8c5d 07df06dc1dbd956a7f10dd1cff1fc0639916c49d 17e744e932dc2f7a410d16cfd635497d26e814fa 46b913bc733c46bf5c9e3e3500a7066d7b1946a5 8c7755698ba53face9b33921b260328be54de611" -DSection=debug -UReplaces -UBreaks
echo misc:Depends= >> debian/tabix.substvars
echo misc:Pre-Depends= >> debian/tabix.substvars
install -d debian/.debhelper/tabix/dbgsym-root/DEBIAN
dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/.debhelper/tabix/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=3663bf2081ff6fbf36141e4e81f2eaea3eebb13d 78b493b45c540d2e60d1646ca8a8d07b83ba80b4 8929b18bf9410f2033bb8685a532aec71352ea6a" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/libhts-dev/DEBIAN/control
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control
dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/control
dpkg-gencontrol -plibhts3 -ldebian/changelog -Tdebian/libhts3.substvars -Pdebian/libhts3
chmod 0644 -- debian/tabix/DEBIAN/control
chmod 0644 -- debian/libhts3/DEBIAN/control
dh_md5sums -a
cd debian/libhts3 >/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
cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/libhts3/DEBIAN/md5sums
chmod 0644 -- debian/tabix/DEBIAN/md5sums
cd debian/.debhelper/libhts3/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/libhts3/dbgsym-root/DEBIAN/md5sums
chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --root-owner-group --build debian/libhts3 ..
dpkg-deb --root-owner-group --build debian/libhts-dev ..
dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root ..
dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.13+ds-2+b1_armhf.deb'.
dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.13+ds-2+b1_armhf.deb'.
dpkg-deb: building package 'libhts3' in '../libhts3_1.13+ds-2+b1_armhf.deb'.
dpkg-deb --root-owner-group --build debian/.debhelper/libhts3/dbgsym-root ..
dpkg-deb: building package 'libhts3-dbgsym' in '../libhts3-dbgsym_1.13+ds-2+b1_armhf.deb'.
dpkg-deb --root-owner-group --build debian/tabix ..
dpkg-deb: building package 'tabix' in '../tabix_1.13+ds-2+b1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../htslib_1.13+ds-2+b1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> -O../htslib_1.13+ds-2+b1_armhf.changes
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-1.13+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-06-14T22:07:36Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
htslib_1.13+ds-2+b1_armhf.changes:
----------------------------------
Format: 1.8
Date: Fri, 27 Aug 2021 22:02:59 +0200
Source: htslib (1.13+ds-2)
Binary: libhts-dev libhts3 libhts3-dbgsym tabix tabix-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 1.13+ds-2+b1
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
libhts-dev - development files for the HTSlib
libhts3 - C library for high-throughput sequencing data formats
tabix - generic indexer for TAB-delimited genome position files
Changes:
htslib (1.13+ds-2+b1) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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211905a67328d790f9786d1427e2a183487d3cd0 4045312 libhts-dev_1.13+ds-2+b1_armhf.deb
1ec9829fe6faa350ef8982fb7e5fdbbc4df34b51 1131932 libhts3-dbgsym_1.13+ds-2+b1_armhf.deb
4bc6916c3c74eb06c9688f655853b8be96eedf6c 338872 libhts3_1.13+ds-2+b1_armhf.deb
1d54c74fd3a1e8e1b3a9ac5e3bf05305f849d270 1438856 tabix-dbgsym_1.13+ds-2+b1_armhf.deb
562149f3ec53a9194f638ba5f70d06376757dbdf 293084 tabix_1.13+ds-2+b1_armhf.deb
Checksums-Sha256:
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58b63fd9abc47a430ddbba9583f29f228423165dee6f76b0888f1308ddba4e7f 4045312 libhts-dev_1.13+ds-2+b1_armhf.deb
35eb7d2f1a0c2cb58d6b804698212d46afd0c1efc1218a41d21de4a0eae65c78 1131932 libhts3-dbgsym_1.13+ds-2+b1_armhf.deb
aff1db55a4b4f86bfb1c74561f94a07d0e29b86ce11b0c55118ec295733fe70b 338872 libhts3_1.13+ds-2+b1_armhf.deb
e7c37bb593fcce67ac1adde1909a49539cf14234d1bc3e8941ec53010e20757e 1438856 tabix-dbgsym_1.13+ds-2+b1_armhf.deb
af5e0933d675f94f93b24bc59d6598c8ae9ada7d42688ccdda7f7261c2c9b81e 293084 tabix_1.13+ds-2+b1_armhf.deb
Files:
f4ff088a35af8882d3caeddfdaa5c9ec 6873 science optional htslib_1.13+ds-2+b1_armhf.buildinfo
ff3af47afbf8f4f9749728dfe33e3089 4045312 libdevel optional libhts-dev_1.13+ds-2+b1_armhf.deb
32a28bbb29bf0059c3d8175cadb8c3da 1131932 debug optional libhts3-dbgsym_1.13+ds-2+b1_armhf.deb
82abcfb204b82c22375c8065362e8f3d 338872 libs optional libhts3_1.13+ds-2+b1_armhf.deb
21b711dbbce0256d3c372bd0694a8b7d 1438856 debug optional tabix-dbgsym_1.13+ds-2+b1_armhf.deb
09e03a3e40dfebfae1ce20f2466ea943 293084 science optional tabix_1.13+ds-2+b1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libhts-dev_1.13+ds-2+b1_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 4045312 bytes: control archive=2012 bytes.
1231 bytes, 27 lines control
2438 bytes, 37 lines md5sums
Package: libhts-dev
Source: htslib (1.13+ds-2)
Version: 1.13+ds-2+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5127
Depends: libhts3 (= 1.13+ds-2+b1), libcurl4-gnutls-dev, libdeflate-dev, 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.
.
For compatibility with sambamba, the internal routine cram_to_bam was
exported, hereto adopting a patch found in guix.
drwxr-xr-x root/root 0 2021-08-27 20:02 ./
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/include/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/include/htslib/
-rw-r--r-- root/root 16081 2020-09-16 10:17 ./usr/include/htslib/bgzf.h
-rw-r--r-- root/root 16837 2021-02-03 10:22 ./usr/include/htslib/cram.h
-rw-r--r-- root/root 12934 2020-09-16 10:17 ./usr/include/htslib/faidx.h
-rw-r--r-- root/root 12877 2021-06-22 11:24 ./usr/include/htslib/hfile.h
-rw-r--r-- root/root 55006 2021-07-07 17:18 ./usr/include/htslib/hts.h
-rw-r--r-- root/root 3989 2020-07-17 12:01 ./usr/include/htslib/hts_defs.h
-rw-r--r-- root/root 11485 2020-05-14 09:28 ./usr/include/htslib/hts_endian.h
-rw-r--r-- root/root 3760 2020-11-30 16:43 ./usr/include/htslib/hts_expr.h
-rw-r--r-- root/root 3944 2019-10-01 23:06 ./usr/include/htslib/hts_log.h
-rw-r--r-- root/root 2533 2021-02-03 10:22 ./usr/include/htslib/hts_os.h
-rw-r--r-- root/root 5605 2020-01-23 10:28 ./usr/include/htslib/kbitset.h
-rw-r--r-- root/root 2828 2019-11-19 11:20 ./usr/include/htslib/kfunc.h
-rw-r--r-- root/root 22899 2020-09-16 10:17 ./usr/include/htslib/khash.h
-rw-r--r-- root/root 4050 2020-08-10 09:46 ./usr/include/htslib/khash_str2int.h
-rw-r--r-- root/root 5135 2019-11-19 11:20 ./usr/include/htslib/klist.h
-rw-r--r-- root/root 3362 2021-02-03 10:22 ./usr/include/htslib/knetfile.h
-rw-r--r-- root/root 3295 2020-08-27 11:09 ./usr/include/htslib/kroundup.h
-rw-r--r-- root/root 8916 2021-05-05 17:01 ./usr/include/htslib/kseq.h
-rw-r--r-- root/root 11480 2019-11-19 11:20 ./usr/include/htslib/ksort.h
-rw-r--r-- root/root 11090 2020-09-29 19:51 ./usr/include/htslib/kstring.h
-rw-r--r-- root/root 8881 2020-07-29 14:09 ./usr/include/htslib/regidx.h
-rw-r--r-- root/root 79223 2021-06-22 11:24 ./usr/include/htslib/sam.h
-rw-r--r-- root/root 15920 2021-04-20 09:42 ./usr/include/htslib/synced_bcf_reader.h
-rw-r--r-- root/root 4942 2020-07-29 14:09 ./usr/include/htslib/tbx.h
-rw-r--r-- root/root 12747 2020-09-16 10:17 ./usr/include/htslib/thread_pool.h
-rw-r--r-- root/root 62511 2021-02-10 11:27 ./usr/include/htslib/vcf.h
-rw-r--r-- root/root 1686 2020-07-11 12:34 ./usr/include/htslib/vcf_sweep.h
-rw-r--r-- root/root 4919 2020-09-16 10:17 ./usr/include/htslib/vcfutils.h
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 4769392 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/libhts.a
lrwxrwxrwx root/root 0 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/libhts.so -> libhts.so.1.13+ds
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 650 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/libhts-dev/
-rw-r--r-- root/root 2680 2021-04-12 10:37 ./usr/share/doc/libhts-dev/README
-rw-r--r-- root/root 2961 2019-12-10 17:59 ./usr/share/doc/libhts-dev/README.large_positions.md.gz
-rw-r--r-- root/root 401 2021-08-27 20:02 ./usr/share/doc/libhts-dev/README.test
-rw-r--r-- root/root 222 2021-08-27 20:02 ./usr/share/doc/libhts-dev/changelog.Debian.armhf.gz
-rw-r--r-- root/root 5871 2021-08-27 20:02 ./usr/share/doc/libhts-dev/changelog.Debian.gz
-rw-r--r-- root/root 24123 2021-07-07 17:18 ./usr/share/doc/libhts-dev/changelog.gz
-rw-r--r-- root/root 5897 2021-08-27 20:02 ./usr/share/doc/libhts-dev/copyright
libhts3-dbgsym_1.13+ds-2+b1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 1131932 bytes: control archive=824 bytes.
573 bytes, 13 lines control
617 bytes, 6 lines md5sums
Package: libhts3-dbgsym
Source: htslib (1.13+ds-2)
Version: 1.13+ds-2+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1241
Depends: libhts3 (= 1.13+ds-2+b1)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libhts3
Build-Ids: 00463a9088228d34203fdacfa2e18408e45c8c5d 07df06dc1dbd956a7f10dd1cff1fc0639916c49d 17e744e932dc2f7a410d16cfd635497d26e814fa 46b913bc733c46bf5c9e3e3500a7066d7b1946a5 8c7755698ba53face9b33921b260328be54de611
drwxr-xr-x root/root 0 2021-08-27 20:02 ./
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drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 12180 2021-08-27 20:02 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-08-27 20:02 ./usr/share/doc/libhts3-dbgsym -> libhts3
libhts3_1.13+ds-2+b1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 338872 bytes: control archive=4040 bytes.
1262 bytes, 23 lines control
972 bytes, 13 lines md5sums
30 bytes, 1 lines shlibs
14553 bytes, 544 lines symbols
67 bytes, 2 lines triggers
Package: libhts3
Source: htslib (1.13+ds-2)
Version: 1.13+ds-2+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 831
Depends: libbz2-1.0, libc6 (>= 2.33), libcurl3-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.1.1), liblzma5 (>= 5.1.1alpha+20120614), libssl3 (>= 3.0.0), zlib1g (>= 1:1.1.4)
Breaks: ivar (<< 1.3.1~), libhts-dev (<< 1.13~), libtabixpp (<< 1.0.0-5~), python3-pysam (<< 0.15~), samtools (<< 1.13~)
Replaces: libhts-dev (<< 1.13~)
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 2021-08-27 20:02 ./
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/htslib/
-rw-r--r-- root/root 9660 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so
-rw-r--r-- root/root 26044 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so
-rw-r--r-- root/root 26044 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so
-rw-r--r-- root/root 13756 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so
-rw-r--r-- root/root 693676 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/libhts.so.1.13+ds
lrwxrwxrwx root/root 0 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/libhts.so.3 -> libhts.so.1.13+ds
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/
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-rw-r--r-- root/root 5871 2021-08-27 20:02 ./usr/share/doc/libhts3/changelog.Debian.gz
-rw-r--r-- root/root 24123 2021-07-07 17:18 ./usr/share/doc/libhts3/changelog.gz
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-rw-r--r-- root/root 1537 2021-08-27 20:02 ./usr/share/man/man5/sam.5.gz
-rw-r--r-- root/root 1857 2021-08-27 20:02 ./usr/share/man/man5/vcf.5.gz
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/man/man7/
-rw-r--r-- root/root 2167 2021-08-27 20:02 ./usr/share/man/man7/htslib-s3-plugin.7.gz
tabix-dbgsym_1.13+ds-2+b1_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 1438856 bytes: control archive=704 bytes.
468 bytes, 12 lines control
403 bytes, 4 lines md5sums
Package: tabix-dbgsym
Source: htslib (1.13+ds-2)
Version: 1.13+ds-2+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1605
Depends: tabix (= 1.13+ds-2+b1)
Section: debug
Priority: optional
Description: debug symbols for tabix
Build-Ids: 3663bf2081ff6fbf36141e4e81f2eaea3eebb13d 78b493b45c540d2e60d1646ca8a8d07b83ba80b4 8929b18bf9410f2033bb8685a532aec71352ea6a
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drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 126032 2021-08-27 20:02 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-08-27 20:02 ./usr/share/doc/tabix-dbgsym -> tabix
tabix_1.13+ds-2+b1_armhf.deb
----------------------------
new Debian package, version 2.0.
size 293084 bytes: control archive=1156 bytes.
997 bytes, 20 lines control
625 bytes, 10 lines md5sums
Package: tabix
Source: htslib (1.13+ds-2)
Version: 1.13+ds-2+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 993
Depends: libbz2-1.0, libc6 (>= 2.33), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.0), liblzma5 (>= 5.1.1alpha+20120614), zlib1g (>= 1:1.1.4)
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 package is built from the HTSlib source, and provides the bgzip, htsfile,
and tabix tools.
drwxr-xr-x root/root 0 2021-08-27 20:02 ./
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/bin/
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-rwxr-xr-x root/root 444000 2021-08-27 20:02 ./usr/bin/htsfile
-rwxr-xr-x root/root 452188 2021-08-27 20:02 ./usr/bin/tabix
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/tabix/
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-rw-r--r-- root/root 1915 2021-08-27 20:02 ./usr/share/man/man1/htsfile.1.gz
-rw-r--r-- root/root 3318 2021-08-27 20:02 ./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: 59232
Build-Time: 2212
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 353
Job: htslib_1.13+ds-2
Machine Architecture: armhf
Package: htslib
Package-Time: 2621
Source-Version: 1.13+ds-2
Space: 59232
Status: successful
Version: 1.13+ds-2+b1
--------------------------------------------------------------------------------
Finished at 2022-06-14T22:07:36Z
Build needed 00:43:41, 59232k disc space