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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Michael R. Crusoe pushed to branch debian/experimental at <a href="https://salsa.debian.org/med-team/samtools">Debian Med / samtools</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/597b83e1a4c767599cca3688403459b2abae046d">597b83e1</a></strong>
<div>
<span> by peterjc </span> <i> at 2014-04-15T11:59:11+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Handle CIGAR N in samtools depad by treating as CIGAR D.
This is not ideal, but is much better than not handling the read at all
(which would happen if the assert didn't abort the command).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/df5b8e7d127b904afe9321d43516aed2d6bccab2">df5b8e7d</a></strong>
<div>
<span> by peterjc </span> <i> at 2014-04-15T13:49:05+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add return value to unpad_seq to allow abort on error
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a22f9794c73a3a25ec763e8c0f038c01fbc60e49">a22f9794</a></strong>
<div>
<span> by uzbit </span> <i> at 2014-07-23T17:10:53-07:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update bam_tview_curses.c
Large scroll up and down with cap K, J</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c8e1a2bf94c48787b26a0e5d4f2b4d3c488ebc07">c8e1a2bf</a></strong>
<div>
<span> by Petr Danecek </span> <i> at 2014-08-13T08:48:13+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>stats: Compute checksum for names/seqs/quals
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2192dda9e2b7bfaf0c31feed65a052ea1e61fc35">2192dda9</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-08-15T11:36:35+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge version number bump from master branch
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e3d4eeeba957986491702c9fddda1d01c5826db7">e3d4eeeb</a></strong>
<div>
<span> by Shane McCarthy </span> <i> at 2014-08-17T17:09:23+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>fix DPR annotation
* Max alleles got changed in 8030ea3 to 5 instead of 4 to
fix a speparate bug, but 4 left at line 127 in bam2bcf.c
when initialising memory. This leads to bug reported in
#274
* Fix this, but also make `B2B_MAX_ALLELES' a constant to
set this number everywhere it is used (@pd3 please check)
* Parsing of tags was broken. the `--tag' options in the
example in #274 should not have been parsed. Should be
fixed now
* Add test output for all `--tags' options
Fixes #274
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a0254acaa445dc336b2ef81736d4ea85eae33a56">a0254aca</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-08-18T16:37:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>No need to initialise array anyway
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a9d452c1934681d47dedbfce4031756ef6c259ca">a9d452c1</a></strong>
<div>
<span> by Christian Krause </span> <i> at 2014-08-18T20:23:34+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>fixes #271
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/904f1f560bb4ff2aa61f6ec1b5ce83613c4b963f">904f1f56</a></strong>
<div>
<span> by Christian Krause </span> <i> at 2014-08-18T20:29:08+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>fixes #272
- consistent use of /usr/bin/env perl shebangs
- consistent use of 'use warnings;' in favor of perl -w
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6099d5707934ecd78cba98a2adf03b2bba202c8e">6099d570</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-08-19T11:05:01+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge stats checksums
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/258b4e60661f687d9ff509fc2b97fe00b37ebb89">258b4e60</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2014-08-19T11:27:35+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Modified the mpileup tests to have local copies of appropriate
reference sequences. All other tests already had this (but
accidentally escaped in some circumstances).
Added a non-existant REF_PATH= to the tests to prevent it using the
default search path and escaping off to the EBI.
See https://github.com/samtools/samtools/issues/279
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f5288ca22e5825b1d4dcd78b4fe90be5b85d67e6">f5288ca2</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-08-20T16:18:27+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Replace bcftools+bcf_filter.sh with new vcf-miniview
Add new vcf-miniview test utility, which reads BCF or VCF and outputs
VCF optionally filtered in the same way that the old bcf_filter.sh did.
The sed -r option used by bcf_filter.sh was not available on OS X, and
an installation of bcftools will not necessarily be available on test
machines, notably when testing via travis.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d0e4a6c8caea9e2f6fd654edbf80100cf82b2302">d0e4a6c8</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-08-20T16:52:02+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Insulate test case from $GREP_OPTIONS
Prevent e.g. GREP_OPTIONS='--binary-files=without-match' from
subverting the expected output.
Perhaps we ought to add 'unalias egrep' somewhere too...
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9579135da9eea608ccb44120ede4534bd8c002e5">9579135d</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-08-21T11:12:59+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update expected output with symbolic "<X>" alleles
Since b14b21933b08ccdf7a777ed4a3529edbb03114e9 mpileup outputs a
symbolic allele rather than a plain "X".
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a7e257d0a8e6050fb738d8e232ac882f198b0f7c">a7e257d0</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-08-21T15:22:56+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update QS values in expected output, and don't truncate them
Following the lead of f85ac7d492ddf7fd54e9849733c2d66adf874938
(around the time of which the QS computation changed), we should be
regression testing the full values emitted for QS.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/eeb4b225c70ae3f09ef2986f8530140c730bcac3">eeb4b225</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-08-21T17:18:30+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge minimal MD5 reference area for mpileup tests
Provide a local reference area via $REF_PATH for mpileup/regression.sh
tests (cf 38eda28b81fd3c176f90a0f03d2645fc891167f0's commit message).
(Note that these MD5 files are truncated versions of their full
sequences; just enough to pass the tests.)
Set REF_PATH to an empty value (but not the empty string, as that
produces the default setting), or in general to point within the test
suite, for tests that exercise it -- currently test.pl and regression.sh.
This makes the test suite self-contained for reference areas, and
in particular prevents travis build testing from trying to access
the EBI reference server. Fixes #279.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/56a4e7454ef04ff9b77dc923d962a084c71a218e">56a4e745</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-08-22T07:59:29+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixes segfault in mpileup when alignment is outside of the ref.
If a read is aligned outside of the reference (possibly due to
reference mismatch or truncation), samtools mpileup will segfault. It
should instead warn, and continue on. This commit fixes this.
Author: Don Armstrong <don@debian.org>
Date: Thu, 22 Dec 2011 17:42:44 -0800
Debian-Bug: https://bugs.debian.org/653042
Forwarded: https://sourceforge.net/p/samtools/mailman/samtools-help/thread/20111223160030.GC30099@chouca.igloo/
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f62826fe3e163b90482d3c2db06d187ea1c2c94b">f62826fe</a></strong>
<div>
<span> by Petr Danecek </span> <i> at 2014-08-26T09:42:03+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Clean after fix in e3d4eee
- free allocated memory
- strncmp not necessary with hts_readlist
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/57e71e72d3638d3505dae1bd6c4d921fb98c8c5d">57e71e72</a></strong>
<div>
<span> by Martin Pollard </span> <i> at 2014-08-27T10:56:11+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix fixmates for supplementary reads
Currently samtools fixmate will incorrectly perceive supplementary reads as
primaries and consequently mess up the pairing information for the primaries.
This commit fixes this by passing supplementary reads through unmodified.
This also updates flagstat to separate out the statistics for supplementary
and secondary reads.
Signed-off-by: Martin Pollard <mp15@sanger.ac.uk>
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7b5a9ea8fa30ff2130a9c1d873b38fc50a00a825">7b5a9ea8</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2014-08-28T16:52:31+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Reduce use of abort, remove assert(fp), pass one string to fprintf not multicall
Reduce use of abort to situations where you might actually want to debug.
Remove assert(fp)'s and replace with proper error messages.
Remove a few instances where fprintf is called multiple times rather than just
passing one string to it.
Signed-off-by: Martin O. Pollard <mp15@sanger.ac.uk>
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f4b63330dab0b374dfefac6ea453fe634100d8e6">f4b63330</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-01T17:17:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge #! fixes to misc/ scripts
Use "#!/usr/bin/env (perl|python)" throughout, to get the interpreter
from $PATH. Use "use strict; use warnings;" in Perl scripts (this merge
commit also re-adds strict in novo2sam.pl). Fixes #273.
(These small changes are not legally significant for copyright purposes,
so years in the copyright notices have not been updated.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/faf4dd6c0230c11dd5d8198c53b0e800a4c68033">faf4dd6c</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-02T16:16:08+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Formatting fixes for better grinding into HTML
In particular, the removed .RE was incorrectly nested.
Also use fancy >= and arrow characters where available.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7d678aaa484aa3198a65198aacf61a8e2c067bab">7d678aaa</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-04T15:09:57+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Recanonicalise test/test.pl whitespace -- USE -b/-w TO DIFF/BLAME
This file had a mixture of 4-space and 8-space tabs, which previously
went unnoticed. Manually re-expand tabs to spaces using the right
number of spaces for each tab.
See notes in fcb8af08a6fd3bfcf195407c4ba5bae528ee326d.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/bc00bde96e60a010f4e1b7c67a26821c3a52e8fc">bc00bde9</a></strong>
<div>
<span> by Petr Danecek </span> <i> at 2014-09-05T07:50:54+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>mpileup: conform to VCFv4.2 spec, version string should be quoted
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1f8267de47f104ee6329a824b7515b0a927508ff">1f8267de</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-09T10:51:50+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Recanonicalise padding.c whitespace -- USE -b/-w TO DIFF/BLAME
This file had a mixture of 1-tab and 8-space indents which previously
went unnoticed. See notes in fcb8af08a6fd3bfcf195407c4ba5bae528ee326d.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/20817a8124198f0fa88f3604f9d2153dd6967da1">20817a81</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-09T12:22:36+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge abort/assert reduction (PR #290)
Also update bam_stat.c and bamshuf.c dependencies accordingly.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a4ca344c6e54641865a42b2ea2b57e9c3cc29309">a4ca344c</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2014-09-09T14:05:40+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixmates ct fix
Only add ct if not already present. (Fixes #276)
Make addition of ct a non-default option.
Signed-off-by: Martin O. Pollard <mp15@sanger.ac.uk>
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f2b42d4ce92c27fa83a3543c0cb5c31a2ee86fe6">f2b42d4c</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-09T14:45:54+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge fixmate ct improvements (PR #292)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8c908dfa7516e13409cad2e71923aef27f8e82e8">8c908dfa</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-09T15:12:15+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove view -Q qual_scale option
It's unclear what it might be useful for. Closes #154.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b67461fa100824e378f9f319036910f322e20482">b67461fa</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2014-09-09T15:43:24+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Free the kstring allocated in bam_fillmd1_core in all cases
Rewrote the logic to avoid unmapped reads bailing out early, negating
the (undocumented) -q and -d options. Fixes #143, closes #293.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ef00bd8688673c4e0d87f31903cfe8e19cd8fbeb">ef00bd86</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-11T13:18:57+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Describe compression level settings
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3d6431d16cb7f21e6c318cc9cecdb0cebe0fa14a">3d6431d1</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-17T06:47:20+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge branch 'debian/experimental' into debian/unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/edc09e477372b7791e7f00734d325f3e8d04c398">edc09e47</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-17T06:54:22+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Prevent Makefile from including local copy of the HTSlib.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/932819f028041d11f70270ec5648f6161095722b">932819f0</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-17T06:58:07+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Build for Unstable.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8a118f663a209ff48f9cc6fa6067c064b019e123">8a118f66</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-17T08:12:12+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Build-depend on libhts-dev...
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7fe3838953f2d5e4cd5384f6fc8077f71511fc47">7fe38389</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-17T15:20:34+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use hash table to merge reference sequence headers
Merge in each new collection of @SQ headers via a hash table rather than
using an O(n^2) approach. Fixes #260.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5c49bf94d90dc1a3027f25f4abc94a7d8edda454">5c49bf94</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2014-09-17T18:06:36+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed samtools flagstat to use the samFile (htsFile) API instead of
bamFile. This means it can now work on sam, bam and cram formats
instead of only bam.
Also added a call to the hts_set_opt CRAM_OPT_REQUIRED_FIELDS to
indicate that we do not need to decode other data fields. This only
affects CRAM at present.
NOTE: This hts_set_opt API is subject to change and usage here is
strictly for testing purposes.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2a40f2ea0df5956ad1da71381d7fef28c494f30b">2a40f2ea</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2014-09-17T18:15:51+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Switch from hts_close to sam_close, for consistency (they're the same
thing underneath).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6b2c8c94f8e25f2e727457c2dfc1785e1d2cfb6b">6b2c8c94</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-18T07:34:47+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Current changelog.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/68ca9776ce01cfb322d5811a39f02547842621db">68ca9776</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-19T16:51:42+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Release 1.1: bug fixes
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f69f412352db56f3f0ac519df3906862f49a5607">f69f4123</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2014-09-22T12:26:29+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Versioned Build-Depends libhts-dev >= 1.0
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0446ed7cae33c2f4faec8969df26f6f702841ff2">0446ed7c</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-23T09:36:05+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Conforms with Policy 3.5.6.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8c928df20f8190d3ce139a074e23536987b285df">8c928df2</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-23T10:07:01+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>samtools (1.0-1) unstable; urgency=low
[ Charles Plessy ]
54ca0c1 Merge with upstream's develop branch.
241a731 razip was removed from samtools.
dc25b81 debian/watch: also track release candidates.
07aaf71 Indicate repository layout in git-buildpackage conf. file.
* debian/control
8bc0fb7 Stop depending on CDBS and quilt.
e613142 Drop static libbam, replaced by the dynamic libhts (Closes: #544976).
b5f284c Build-depend on tabix for the regression tests, that use bgzip.
9febad6 Recommend python since samtools installs a python script in /usr/bin.
0446ed7 Conforms with Policy 3.5.6.
* New package samtools-test
7293cca Create a test package for the test data.
6bd7b89 Adjust install file for two-package build.
caff5f5 Clean before installing test files (this removes compiled files).
* debian/rules
c930cbb Use Debhelper instead of CDBS and rely on the new upstream Makefile.
845581d Adjust for dynamic linking.
d859052 Indicate path to packaged bgzip.
cb23517 Mimick Makefile's CPPFLAGS.
aee1c6c Allow parallel building.
edc09e4 Prevent Makefile from including local copy of the HTSlib.
* debian/patches
f73d764 d062687 Refreshed patches.
2c52f6a 61ac2c5 Forwarded patches on GitHub.
b8eb378 Dropped fix_example_makefile.patch, obsolete.
66079b9 Correct path to python interpreter.
218c1c1 Modify Makefile to facilitate dynamic linking.
[ Andreas Tille ]
f69f412 Versioned Build-Depends libhts-dev >= 1.0
-- Charles Plessy <plessy@debian.org> Tue, 23 Sep 2014 09:36:27 +0900
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c87f8ce95e97ca11d98309812bc02c2c0c988190">c87f8ce9</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-23T18:31:59+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add autopkg tests.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1f661b25822072560bde42a3b591d2931c5cdd61">1f661b25</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-23T18:32:48+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Current changelog.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/db22ee99d01d32a3635e3d78a6667a249a6fffd3">db22ee99</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-23T17:16:19+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge version number bump from master branch
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b7c4b4d05154887ec8587165c6da505aad024f52">b7c4b4d0</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-24T14:28:12+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Ensure usage tests have a terminal on stdin
Subcommands (starting with samtools stats) given no arguments choose
whether to filter stdin or to display their usage depending on
isatty(STDIN_FILENO). When testing that usage messages are produced,
ensure commands get a terminal on stdin; otherwise skip the tests
if a terminal cannot be arranged. Fixes #300.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c448d4848f865dbebe33bd6cd520f66fb5745986">c448d484</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-25T08:22:09+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge tag '1.1' into debian/unstable
Bug fix release
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d12ab1ed118c324825bf3bae9996bbe59862f9d7">d12ab1ed</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-25T08:22:21+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge branch 'develop' into debian/unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7c50b7b7bf5a47a81b0a8c355c634600bcfe7291">7c50b7b7</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-25T08:54:27+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Removed python-wrong-path-for-interpreter.patch, solved upstream.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/dcc1da7a658c5739aee7144e5e92c6b93db09cdc">dcc1da7a</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-25T08:55:37+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Removed sed command redundant with patch dynamic-build.patch.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/91356d65b732a7d22a7fff994f9c6d17d75568e3">91356d65</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-25T09:05:17+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>samtools (1.1-1) unstable; urgency=medium
c448d48 Merge tag '1.1' into debian/unstable
d12ab1e Merge branch 'develop' into debian/unstable to solve issue
with regression tests needing a pseudo-terminal.
See https://github.com/samtools/samtools/issues/300
c87f8ce Add autopkg tests.
7c50b7b Removed python-wrong-path-for-interpreter.patch
(issue solved upstream).
-- Charles Plessy <plessy@debian.org> Thu, 25 Sep 2014 09:04:20 +0900
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/281bf0a1756abf4b0527877db37d01dbdf6bd764">281bf0a1</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-25T11:52:12+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Recanonicalise regression.sh whitespace -- USE -b/-w TO DIFF/BLAME
This file had mostly 8-space tabs, which previously went unnoticed.
See notes in fcb8af08a6fd3bfcf195407c4ba5bae528ee326d.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6c2d9cd543036264833eca4d3e1a3483d78cc914">6c2d9cd5</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-25T21:39:17+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Build-depend and recommend libio-pty-perl for the regression tests.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d3946de853e86ecd11a7a15dab9445d364c65d37">d3946de8</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-09-25T21:40:28+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Current changelog.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9c4099fb24e1b48524211e89eed28279b720ab8d">9c4099fb</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-09-29T13:51:26+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Set output file threading only if there is an output file
In particular, there is no output file with -c. Fixes #302.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6ce5671a6ef57e75490e4c3d6dbded71c6612ad3">6ce5671a</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2014-10-01T17:52:37+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Make autopkg test depend on tabix.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/29395a567c043e7ff530f112977e43a71893ad8a">29395a56</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2014-10-01T11:36:23+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed a buffer overflow when dealing with cigar strings ending with a
deletion.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/089ecbe7075cb41b34d75ae189e0f289bb131f0f">089ecbe7</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2014-10-01T12:06:29+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Improved fix to mpileup. The previous one just skipped bases where we
have no quality. This still includes them in the pileup, but with 0
qual instead.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/418fc0c642bbdabef9f4ed4054200c0f47d4372d">418fc0c6</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2014-10-01T12:10:40+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Also fix buffer overrun on data where the sequence is "*".
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2fac99b5f31413454e1eaf29eca4a0cb6ba168db">2fac99b5</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2014-10-01T12:14:33+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed up test data, now that it correctly outputs "n" instead.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/056ae75d01769d8ec70513e1fde67ce139fab96f">056ae75d</a></strong>
<div>
<span> by pd3 </span> <i> at 2014-10-01T13:26:34+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge pull request #306 from jkbonfield/mpileup-fix
Mpileup fixes</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/59c56f0b50c4283e23527d4e3388e903a07b5063">59c56f0b</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-10-06T11:37:03+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Man page formatting fixes
Use hyphens to introduce options rather than en dashes
(addresses samtools/www.htslib.org#5 for samtools man page).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5ac61a295de0ecc29f4b3597eac69b0ab4f24ecb">5ac61a29</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-10-08T10:33:51+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Write failure messages to stderr
No difference by default, but enables highlighting the failures or
capturing them by redirecting stderr.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6f1c154dbfd34d2816ded168a731592a62217bf9">6f1c154d</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-10-10T17:03:21+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Maintain HEAP_EMPTY invariant when an input is empty
Ensure h->b is NULL when we hit EOF on the first read, just as it is
when we hit EOF later in the file. Fixes #309 and also prevents a
memory leak for an input file with no records.
Also use bam_init1()/bam_destroy1() instead of creating and destroying
bam1_t structs by hand.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d2e8d7ace9ebf5cd27dfb2d7cbe34d2e7be607c1">d2e8d7ac</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-10-20T13:04:28+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Avoid using htsFile is_foo bits directly
Use the new public hts_get_format() facilities. Requires htslib
commit 529ca88071e775a488e4108945d5bd863a4190f0 / version 1.2 or later.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/45801506eb6b241b46ff42056f065e01d830a20a">45801506</a></strong>
<div>
<span> by Petr Danecek </span> <i> at 2014-10-21T11:28:18+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Reflect changes in htslib API
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/01465e80d9c9289e23d6074a594309447c1d1847">01465e80</a></strong>
<div>
<span> by Peter Cock </span> <i> at 2014-10-29T16:11:45+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix typo in 'samtools flagstats' output
supplimentary --> supplementary
Reported by Daofeng Li on the samtools-help mailing list:
http://sourceforge.net/p/samtools/mailman/message/32983845/</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6c170712cd5d05055c4794a91c3c6e09c5334343">6c170712</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2014-10-30T10:24:16+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added a test for specifying the reference via samtools -T. This
appeared to work in our previous tests, but did not due to the code
sneakily reverting to the @SQ UR: field instead.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c02491f07d9de213e72613158de12f316ff2c7ae">c02491f0</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-11-03T16:06:29+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge origin/develop, prefering avoiding using htsFile internals
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/dc1f4389fe0eaabb45764c9bf06c47fbfd23f5df">dc1f4389</a></strong>
<div>
<span> by Petr Danecek </span> <i> at 2014-11-03T16:15:07+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>stats: Calculate mismatches per cycle for unclipped length
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6b249e2c682d22e5f1ffbbc6b51d62f8db823bf5">6b249e2c</a></strong>
<div>
<span> by Petr Danecek </span> <i> at 2014-11-03T16:15:12+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge branch 'develop' of github.com:samtools/samtools into develop
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4a2320a4130fffe789986dc4c4977a637ea1b374">4a2320a4</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-11-03T17:45:04+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Avoid "my" variable redeclaration [minor]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a25229a939999a3c065a823a20824cb0940e61d5">a25229a9</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-11-04T10:42:47+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Prevent warnings when compiling on a 32-bit host [minor]
Avoid "%zu" as this C99 library functionality is not supported by MSVC.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c61d8d1ed100fbe03b98f4b30f1f3943dce29305">c61d8d1e</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-11-04T14:49:29+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge origin/develop into develop
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/635336737be82fe922cbb33a9307932c53f8c097">63533673</a></strong>
<div>
<span> by peterjc </span> <i> at 2014-11-05T12:00:21+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>samtools bam2qf option to force FASTA or FASTQ output
This addresses issue #313 - the current behaviour (left as the
default) produces a mixture of FASTQ and FASTA depending on if
each individual read has quality scores or not.
While some tools/parsers will handle mixed files like this, others
will have trouble. This is a problem with systems like Galaxy with
a strict datatype system.
I wanted to use -O for the new output format argument (to follow
the pattern set in samtools sort/rmdup/fixmate) but that is already
taken for the original quality option.
Note that if samtools bam2fq is called forcing FASTQ output, this
currently will use a default PHRED quality score one 1. This value
might make sense to add as a further command line option?
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/76300af95188984555747428a59c59bd6366a7f7">76300af9</a></strong>
<div>
<span> by peterjc </span> <i> at 2014-11-05T16:07:36+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Set default FASTQ quality with samtools bam2fq -v INT
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/bca67a952cb2949645a6a7f51a05b55b27898edf">bca67a95</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-11-12T17:32:15+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Convert bam2bcf_indel.c to use the htslib API directly
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9e3bbcf0e2d30631627b50c53504ab8a41138510">9e3bbcf0</a></strong>
<div>
<span> by Martin Pollard </span> <i> at 2014-11-12T17:38:21+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update comment documentation for bam_mate
Clarify how we now handle supplementary reads and note limitation.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/19c9f67b4d28a25d61d1a5dd1949ea3a238ddad1">19c9f67b</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-11-18T09:23:55+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove unused kaln.c, kaln.h global aligner
The kaln global alignment functions have been unused in
bam_md.c since 51f014165fb63b2b9b86db80ea4681f9351453a1 and
bam2bcf_indel.c since bf8b35cc189c6c846f01752f9e9500a3c08cd9b1.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/29b03673d619dfae2c95c8414e1e0dc0773db72d">29b03673</a></strong>
<div>
<span> by peterjc </span> <i> at 2014-11-20T09:57:09+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Replace cryptic 'minQLen' with real description
[Modified from Peter's suggestion: as l_qseq == cigar2qlen, we don't
need to mention "mapped length" or "CIGAR".]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8dd3761a43012b73fa66daebee65de05464c2d51">8dd3761a</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-11-24T10:13:48+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use bam_init1/bam_destroy1 instead of creating/destroying by hand
Prefer explicit NULLing to historically non-portable memset obscureness.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3fdca5b6e59b855c37f97885e822e746c270c6e8">3fdca5b6</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-11-27T10:44:21+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Make samtools merge work with SAM input files
The iterator API doesn't (yet) work with SAM files, as there's no way
to provide the file's headers when initialising or using the iterator.
For SAM files (in the absence of -R REGION), keep the headers around so we
can use sam_read1() rather than sam_itr_queryi(HTS_IDX_REST)/sam_itr_next().
(This will likely be followed up with an option to write SAM output.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5d6a1e32dc82d18329850bcff040ac388e38bb87">5d6a1e32</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-12-02T10:27:12+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Avoid crashing on unopenable files [minor]
Akin to fclose(), sam_close() requires the file pointer given to it to
be non-NULL; akin to free(), hts_itr_destroy() does not. Fixes #327.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7f47a7cca27b1a3cbf4bf34fecca9cb3c730cda5">7f47a7cc</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-12-09T13:48:23+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Parse mpileup -r region against the right file's headers
Restore the code prior to a bug introduced in e7ae7f96c7e78a2dd6eabdaed57037c483951929.
Amongst other things, this ensures that files without the given
reference sequence are reported as failing to parse the region.
Move the setting of data[i]->h lower in the loop to prevent similar
bugs in future. Ensure that data[i]->iter is always explicitly set.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f3f3d6d78e3a982822c8c33b94639597887803a4">f3f3d6d7</a></strong>
<div>
<span> by John Marshall </span> <i> at 2014-12-11T17:51:23+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Large chromosome test case now passes
Fixed by samtools/htslib@ce1a547f0e01d32fbffb62efbcca51c6ddc77d34.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c06f698c1b98d10e8619f967fc94e07077a40644">c06f698c</a></strong>
<div>
<span> by Martin Pollard </span> <i> at 2014-12-16T15:47:56+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add a few comments to pileup and errmod code, move some existing ones to slightly better positions.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/311926c74331a1e49f700b271e965c6d99445879">311926c7</a></strong>
<div>
<span> by Gianluca Della Vedova </span> <i> at 2015-01-06T16:34:02+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix typo.</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f0c42fee1d73a12919f09b4eaf3b66b3e22b4a52">f0c42fee</a></strong>
<div>
<span> by Nathan T. Weeks </span> <i> at 2015-01-09T15:58:42-06:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Vastly improve performance when many header lines
On at least systems with glibc, regexec() performance suffers greatly
for long search strings. This greatly impacted the runtime of samtools
merge when merging bam files with many (hundreds of thousands or
millions) header lines.
This fix replaces the use of regular expressions in pretty_header() with
string.h functions. Whereas pretty_header() previously could take days
to process over 6 million header lines on systems with affected regular
expression implementations, it can now complete in under a second.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2bcfffdcd3a77887bd4675b21d799e8a9b71facc">2bcfffdc</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-01-12T14:23:38+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added various hts_set_opt calls to set the CRAM_OPT_REQUIRED_FIELDS
and CRAM_OPT_DECODE_MD options to avoid doing unnecessary decoding
work.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a513827743e1ed9be041bd62a44ea2dcd083aef2">a5138277</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-01-14T13:56:59+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge pull request #299 from jkbonfield/cram3
Cram3 updates</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/581e707385b2e7f84592271693f7e19bec86821d">581e7073</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-01-16T13:02:15+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>bamtk.c requires only hts_version(), not <bam.h>
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/446aae08e76a8b0e61b42f9f2e6a2126c3462179">446aae08</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-01-27T09:01:37+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Happy New Year
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e2ce81d42fbd02a923758e1e859f8a502019d2d4">e2ce81d4</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-01-28T14:17:49+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added checks to sam_hdr_write() return value.
Samtools view no longer blindly continues when it failed to write the
header. This avoids silent creation of broken CRAM files when the
reference sequences fail to be processed correctly.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c5df8be21701167cf02fbf3c061f4ee9bba5a2c1">c5df8be2</a></strong>
<div>
<span> by Nathan S. Watson-Haigh </span> <i> at 2015-01-30T15:12:40+10:30 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added 'insert size' to the head of the IS section
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0cc7b47916844de33e1455c285dbe5859ecb314a">0cc7b479</a></strong>
<div>
<span> by pd3 </span> <i> at 2015-01-30T08:38:29+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge pull request #342 from nathanhaigh/develop
Added 'insert size' to the head of the IS section</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8f5033217d9ae2d8ff6d73c87ea64ba3c9bca247">8f503321</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-01-30T15:26:37+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Documentation: Updated REF_CACHE location details.
The new semantics for default REF_PATH and REF_CACHE are described.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/255f97daffd3a27d7b063e991a993f47ad6186cf">255f97da</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-02-02T15:18:41+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Release 1.2: various bug fixes
Also added notes about running against an alternative zlib library.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2e74fb81ef97c7c5d8f60ed2aa690c353d6e3715">2e74fb81</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-02-02T16:32:09+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge version number bump from master
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f8a62748b2225ecd361fd041232a6f8c49878097">f8a62748</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-02-04T13:54:08+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix typo -- hat tip @mcshane
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/12c4cba0be691e7772ba95a12e40de24d77bc228">12c4cba0</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-02-13T09:54:46+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed NM calculation for deletions partially off end of ref.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/76870cc4b0489b46777724a79faf20f1e7d740b7">76870cc4</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-02-19T12:34:05+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Travis builds clone corresponding htslib branch
Rather than always checking out htslib's develop branch, check out a
corresponding branch with the same name if there is one over there.
Default to github.com/samtools/htslib, but allow this to be overridden
e.g. by those who have also forked htslib.
Clone a little faster with --depth=1.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9c6a5c1bfa2298fdb7ae7b5e714f2dc90d31da22">9c6a5c1b</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-02-20T11:32:21+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Replace bam_nt16_nt4_table[] by htslib's seq_nt16_int[]
An equivalent was added in samtools/htslib@9a88137bb6d7e25e82c3cd64a0a54433585a2e4e,
so re-add bam_nt16_nt4_table[] to bam.h in terms of it, undoing the somewhat
misguided 24a52ab78d63e5586f33cc1f57cc2a1e9f2caad7.
Old API code uses bam_nt16_nt4_table[] from bam.h; direct htslib-API code
uses seq_nt16_int[] directly. Nuke all extern declarations.
[NEWS]
* Restored bam_nt16_nt4_table[] to legacy API header bam.h
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f46e5b7bfa41283af2f3a071d959382129a3d4fa">f46e5b7b</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-02-20T15:06:29+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Implement calmd directly against the htslib API
Remove mode_r and ignore the -S option, as input file formats are
now automatically detected.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/78927b708d76e4e959fbf463aa6b92d5477bf614">78927b70</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-02-20T15:58:55+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix calmd -u to write level-0-compressed rather than raw BAM
samtools/htslib@818a5ed171eb0cc3667a6c01845fca19a17d4478 changed the
meaning of hts_open(fn, "wu") but bam_md.c was not updated accordingly
at the time.
Also added test case. Hat tip @sb10.
[NEWS]
* Restored previous "samtools calmd -u" behaviour of writing compression
level 0 BAM files. Samtools 1.0 to 1.2 incorrectly wrote raw non-BGZF
BAM files, which cannot be read by most other tools. (Samtools commands
other than calmd were unaffected by this bug.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/eb21ebaa7bae9d56175009a7b0dfa4008df6cd1b">eb21ebaa</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-02-23T15:20:53+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix @SQ-LN headers to match actual .fa lengths
As of samtools/htslib@83190e9076ac8ce0ec51de2688a8845844df2ad3, htslib
fixes up @SQ reference sequence lengths that disagree with the actual
sequences found in the reference.
The reference sequences for these test cases were truncated from the
data they came from; reflect that in the test case data.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d0c02de3908a148bcda58e19827c0f94cd5baaae">d0c02de3</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-02-23T17:07:29+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update MD/NM as if by using calmd
As of samtools/htslib@1f3ef0ae24bca8116b85adb8e584f1e497786687, a trip
through CRAM updates MD/NM tags for reads off the end of a reference
sequence. Update such reads in the test data.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b7ac1e2819ab85d5950eb2ce02434aa422fe39ed">b7ac1e28</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-02-24T10:14:51+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added error checking around hts_set_fai_filename() calls.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/356ca470d4aca082497f74587151675c8d518ccf">356ca470</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-03-05T16:43:28+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Clarify "SAM files differ" error message
Print to stderr for potential highlighting, and also print the
differing lines in question so one can see what the problem is.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/918a5676e03ac48fa151359d392acb10aaef1ebb">918a5676</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-03-06T15:29:32+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>For 0.1.x compatibility, "fixmate - -" writes BAM
Pipelines like "... | samtools fixmate - - | ..." worked fine with
samtools 0.1.x but fail ("cannot determine output format") with 1.x.
When no -O option is used, default to BAM as per 0.1.x rather than
failing.
[NEWS]
* "samtools fixmate - -" works in pipelines again; with 1.0 to 1.2,
this failed with "[bam_mating] cannot determine output format"
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8a5a91a4b8618ca2e1b818afa3e25b210b57441b">8a5a91a4</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-03-09T10:26:04+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Writing SAM files may leave htsExactFormat as text_format
[NEWS]
* Fix legacy API's samopen() to write headers only with "wh" when writing
SAM files. Plain "w" suppresses headers for SAM file output, but this
was broken in 1.2.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0df98194863cea022f1b067cb9d4f55eab895d32">0df98194</a></strong>
<div>
<span> by student-t </span> <i> at 2015-03-09T10:41:37+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update 00README.txt
Fixed spelling.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a83ac9da65f1acd49b9885fcb2305304f39d22ee">a83ac9da</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-03-09T11:28:15+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add sam_index_load() and samfetch() to legacy API
Hat tip @drjsanger.
[NEWS]
* Add legacy API sam.h functions sam_index_load() and samfetch() providing
bam_fetch()-style iteration over either BAM or CRAM files. (In general
we recommend recoding against the htslib API directly, but this addition
may help existing libbam-using programs to be CRAM-enabled easily.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7dc40b4fe2d58e5fe228fc67f2f19631dd2e6eb2">7dc40b4f</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-03-09T11:37:51+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>[tview] Use iterator directly instead of our own sam_fetch() function
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e91985a784e9aa2787be4dfb5a4aa53ad6657acd">e91985a7</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-03-09T16:20:23+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge pull request #361 from samtools/samfetch
Add sam_index_load() and samfetch() to legacy API</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e1714f69e4d41c029e9f5eb534b8089509006048">e1714f69</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-03-11T12:37:14+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Changed from a local misc/md5.c to using the API in htslib.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/329c05f683ae27a19eb845b7425de33ba1d3afb7">329c05f6</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-03-11T12:37:14+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Changes to support the updated htslib md5 interface.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5dfdf2ed63bf7a666fe4bf93d558acb919f89432">5dfdf2ed</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-03-11T12:40:39+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Rebased and changed to use updated hts_md5_hex.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d4f5b07e91b56e909c34d2e8b4bee8327101aa26">d4f5b07e</a></strong>
<div>
<span> by Shaun Jackman </span> <i> at 2015-03-18T12:07:16+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>wgsim: Clarify that -S0 seeds with current time
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ad9d270ffde19e5c2c53382fc8c881560473261f">ad9d270f</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-03-18T14:01:24+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Canonicalise md5sum-lite.c whitespace
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b542645c62c6719e8b561e1eaa0c54ab9fe20e27">b542645c</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-03-18T14:57:13+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge use of htslib's MD5 API (PR #354)
Requires samtools/htslib@3accd1934472e2bdd501404f4c1a2e570f868cd1.
Updated remaining hts_md5_hex() call to final version.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/dd76533d67b0495dc84c2bbdfce857fee97cf334">dd76533d</a></strong>
<div>
<span> by Shane McCarthy </span> <i> at 2015-03-19T10:22:40+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>samtools dict command to create a sequence dictionary file from a fasta
ala Picard CreateSequenceDictionary
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/016c62b02b1f60311ee4d3ac8c7957560fc4227e">016c62b0</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-03-19T10:28:26+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>[stats] Implement init_regions(), disabled by missing header API
In fact all init_regions() needs to do is look up a tid, for which
an API function is already provided.
[NEWS]
* samtools stats --target-regions option works again
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f995b7195a116076a3e4dc0237a84a529a18766a">f995b719</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-03-23T16:24:55+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>[Makefile] Use user's CPPFLAGS/LIBS variables
Remove INCLUDES and add EXTRA_CPPFLAGS for our own various options that
need to stay set even if the user overrides CPPFLAGS. If we end up with
necessary compiler or linker options or libraries, we'll add EXTRA_CFLAGS,
EXTRA_LDFLAGS, or EXTRA_LIBS accordingly.
Rename LDLIBS to LIBS; it seems that LDLIBS doesn't particularly
exist outside GNU Make's built-in rules. Instead LIBS is configure's
conventional variable for the purpose, so is the right thing to use
for a user-visible variable.
[NEWS]
* Samtools's Makefile now fully supports the standard convention of
allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden as needed.
Previously it listened to $(LDLIBS) instead; if you were overriding
that, you should now override LIBS rather than LDLIBS.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/438e92d308088d803a598122a1f584338cc65e92">438e92d3</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-03-28T11:03:45+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge new dict command (PR #366)
[NEWS]
* new samtools dict command, which creates a sequence dictionary
(as used by Picard) from a FASTA reference file
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9f3da0630ca16106f60945504decbc5a8aab2e9c">9f3da063</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-03-30T13:51:57+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Handle hts_parse_reg() returning NULL
After samtools/htslib@62e4541d8cbfb4e8250eb42d454e714da9d369d5,
hts_parse_reg() returns NULL when the region could not be parsed.
For an unlikely reference sequence name like "foo:a" this could be a
request for the whole chromosome, so (because we can) handle this case.
Also take advantage of the NULL return to distinguish unknown sequence
names from malformatted regions in error messages. Fixes #353.
For truly ridiculous sequence names like "foo:10-50", users will need
to write whole-chromosome regions as "foo:10-50:1".
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ca44680262884c9f14b09b525b3a55e37e583ec7">ca446802</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-03-30T15:07:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>[flagstat] Print "N/A" rather than NaN percentages
Fixes #365. Also improve whitespace around percentages.
Also update bam_stat.o dependencies.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c94d93780b474b1c2abcc47aa15f00e029475b9b">c94d9378</a></strong>
<div>
<span> by Petr Danecek </span> <i> at 2015-04-08T07:31:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>stats: make cram index work
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/84d070296492e86e450c4f2abda8e9521ccd6da2">84d07029</a></strong>
<div>
<span> by Shane McCarthy </span> <i> at 2015-04-13T13:49:35+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>copy RG, BC and QT tags to the FASTQ header
bam2fq: pull in option from @lh3 htsbox repo to copy RG, BC and QT tags to the FASTQ header
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3f3dbeff7d4d82625ae8d5db871bfec88b018173">3f3dbeff</a></strong>
<div>
<span> by Shane McCarthy </span> <i> at 2015-04-13T13:49:35+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>add bam2fq -t option to man page
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/33f055c687f3609f7f21e48174feaab79b9133c5">33f055c6</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-04-13T15:25:37+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge bam2fq RG/BC/QT copying (PR #325)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/428b8e29addbf4d3eb0763250cd1904db1156492">428b8e29</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2015-04-13T17:25:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Make bam_merge_core2 check that sam_index_load() worked.
Add a missing check for a NULL return value from sam_index_load(). This
prevents a segfault when running samtools merge with the -R option on
files that have not been indexed. Instead a message is printed to stderr
and samtools returns a non-zero exit code.
Fixes issue #377.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/23bbfd700d038b85ebc82dfc233fc219c4ff601e">23bbfd70</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-04-14T12:44:57+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Regression.sh fix and mpileup hts_set_fai_filename fix.
Fixed the regression.sh to report failures when a program fails (as
well as succeeds but now gives a different result, which was the
original expectation).
Also fixed the mpileup command causing these regressions. It
previously called hts_set_fai_filename() on NULL filenames.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/738e4026f7edbd880b3142ad6722841118c4aef1">738e4026</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-04-14T12:44:57+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added -a option to samtools depth.
This produces depth information for all positions rather than just the
ones covered by a sequence. Specifying -a twice will additionally
include depth information on reference sequences not covered by any
read in the file.
Added test cases too, but documentation is (still) absent.
Fixes #374
[NEWS]
* Added -a option to samtools depth to show all locations, including
zero depth sites.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/92899ba6e7e0bf73d1295071014a8c135b1ef232">92899ba6</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-04-14T13:46:27+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added missing test output files for samtools depth.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c03c811be6f317e16d4ede0273d9d23a38d381c1">c03c811b</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-04-14T13:48:57+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Swapped bam for sam in samtools depth tests.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b94f0f2bc9c9b0e04c8a85b8673057a633d1b8df">b94f0f2b</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-04-14T14:07:20+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added "samtools depth" check outputs to testclean target
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f65869ca27fbffceee459e499f1e91f139733dbe">f65869ca</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-04-14T16:09:43+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Extra care for floating point comparisons to avoid 32-bit "make check" failures.
Fixes #305
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/15f26e821f73ee02f58c4a496a998fb86ade3f54">15f26e82</a></strong>
<div>
<span> by Petr Danecek </span> <i> at 2015-04-16T14:05:48+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Resolved merge conflict
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/43ca26c42891523363b5aa9839fa711cb7bf21bd">43ca26c4</a></strong>
<div>
<span> by Petr Danecek </span> <i> at 2015-04-16T14:07:02+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Reored usage string
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2bf045de02652867ae9b5a46697b277cc82a80a0">2bf045de</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-04-21T16:45:31+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Do min_frac comparisons as double rather than float
This suffices to make x87 also produce the expected results for
humanely-readable min_frac values such as 0.6. Fixes #305.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ff95462d4fa3e19dca10d7a32ac977c6c4d7e77c">ff95462d</a></strong>
<div>
<span> by Joshua Randall </span> <i> at 2015-04-27T10:05:55+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Adds missing sections to samtools man page
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c404615a4e7efb79362895a2964139bd482153e3">c404615a</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-01T17:13:45+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added --output-fmt-option and --input-fmt-option to merge, sort and view.
Also where absent added --output-fmt and -O too. These allow control
of the CRAM files being generated. For example to sort a BAM file into
a CRAM file (previously not possible), specifying version 3.0 using an
embedded reference, we would use:
./samtools sort -@ 8 --output-fmt cram -T /tmp/_ \
--output-fmt-option version=3.0 \
--output-fmt-option embed_ref \
-o /tmp/foo.cram /tmp/foo.bam
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/317e6c91ab1475ac8a1a2d2f3357bc5042ea5e16">317e6c91</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-01T17:49:10+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added --input-fmt-options arg.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0736a655e1692b10d012214162b8b2aec0040d89">0736a655</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-05-06T14:04:42+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge pretty_header() performance improvement (PR #337)
Renamed copy_records()/et al to copy_headers(), as in this code "record"
usually means a bam1_t rather than a header. Simplified the any-other-
headers loop to iterate over lines directly. Fixes #373 too.
[NEWS]
* Merging files with millions of headers now completes in a reasonable
amount of time (#337, #373; thanks to Nathan Weeks)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5c3b72714acf36506a2ad8429927b502ac8966c1">5c3b7271</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-05-06T14:24:02+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge x87 floating point precision workaround
Ensure that indel calculations work the same way on x87 as on various
64-bit IEEE platform. Fixes #305; we tried several fixes, as reflected
in this multi-way merge. FLT_EPSILON version preserved for posterity,
and in case we need to revisit this.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7b5c26c8783575d208b81473755635214f122c2e">7b5c26c8</a></strong>
<div>
<span> by Shane McCarthy </span> <i> at 2015-05-07T14:58:45+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>allow samtools merge with one input file
* allow samtools merge with one input file
* slight update to usage docs to reflect this
* test that runs merge with one input file
* fix minor bug when using `-r' option to setting RGID from filename -
now strips `.bam', `.cram' and `.sam' extensions.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3023e2c53d1a3188d625335bfd7b71a843af01c2">3023e2c5</a></strong>
<div>
<span> by Sendu Bala </span> <i> at 2015-05-12T11:56:37+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>added pipe input support to plot-bamstats: use "-" as the bamcheck filename
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/75ba5410abb97766c21c6f2f5538507d1ad9bd90">75ba5410</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-05-12T14:18:27+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add samtools 1.0 faidx RAZF->BGZF note
This should have been mentioned at the time...
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e8f27a32bae18b04f8da8e5a367e68a42096fece">e8f27a32</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-05-12T14:18:27+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge @CO headers
In trans_tbl_init(), copy @CO headers to the destination. Possibly
unknown non-standard headers (if any) should just be copied similarly.
The output file still gets an @HD header from the first input file only.
Update test cases correspondingly. See also #390.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1f577c41b612afe765f4bdd601fc63e27dda1a46">1f577c41</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-14T12:28:11+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Rationalised the long option handling for "global" options.
There is a new hts_open_opts too that takes an option structure. This
is a change in behaviour as the former code used hts_open followed by
an hts_opt_apply call to apply the options to the file handle.
Many more sub-commands to-do still. This is largely a patch for the
option infrastructure and a few subcommands to test it with.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a515c2ce3e517fce6ef88e29416b0f57876d118a">a515c2ce</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-14T15:25:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Changed bamshuf to use sam_open instead of bgzf_open so it can handle all formats.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3022021067063aa242cfb0da2015b29792185656">30220210</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-15T11:28:46+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>More --output-fmt-options: fixmate and bamshuf.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/14e9a5ec4459edb04e8ea43f993b3c4fcf749a24">14e9a5ec</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-15T14:42:53+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed bam split test harness.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/942d55f8680b5ff8456cca652b196138ff2300e9">942d55f8</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-15T15:55:48+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Updated to keep in sync with htslib changes (hts_open_format et al).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ff29be9a5e4ed00b1bf3d3acee8370eedb0cd00a">ff29be9a</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-15T17:37:44+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed bamshuf to use BAM level 1 for temp files and .%s for final output file.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/dd779efdc98734db8176d37a45a276becf3bfc4c">dd779efd</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-15T17:56:31+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed use of hts_opt_add following change to htsFormat struct.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4e2cdee27878789c2a6c08af89ce9fa129b73299">4e2cdee2</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-15T17:57:01+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added --input-fmt-option to bam2depth.
Also fixed report of errors.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b0525f3e74836004f522c96a26bc7e660e032de4">b0525f3e</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-18T09:41:46+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added pointer to our own published zlib benchmarks.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/367d754fccbcd1995737e04c805740cb340dd861">367d754f</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-18T14:49:08+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>More sub-commands with --input-fmt-option.
This provides a way of specifying references to CRAM where the command
doesn't accept a reference and to specify the number of decoding threads.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/723ee29f4b82af87ec1385a3d9a0686871c450ba">723ee29f</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-19T16:36:56+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed bedcov usage. (I'm impressed the test harness spotted this!)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/52094e191052f3ea9257f9539ca1a046a134479c">52094e19</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-19T17:38:28+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Improved usage of CRAM_OPT_REQUIRED_FIELDS.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/aa7eb08e86b6be59f222247e1000421aa67f7a92">aa7eb08e</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-20T09:48:33+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>bam2fq: fixed -O with CRAMs. Also now detects decoding error (BAM or CRAM).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b9af7eb93781755a0c99be7300e02a675dcab7a7">b9af7eb9</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-20T17:05:51+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>More long option handling.
Removed the --verbose global option (it was only there as a test for
options with no argument).
Added --reference option which applies it to both input and output
format.
Updated a few commands from the older sam_open / hts_opt_apply syntax
to sam_open_format instead.
Added more error checking to marge, sort and split.
Samtools split and bamshuf now use .bam as the default extension again
when no format is specified.
Samtools cut_target now handles both sam and cram format too.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ae2332da5048605c7313de729588adfdea24a985">ae2332da</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-20T17:48:57+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed an issue causing mpileup --rf and stats --help to fail.
This was caused by the new long options and assign_short_opts only
modifying the first fields rather than expliitly looking for the new
options by name.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/af658fbbc1e0b7e1aa2ac6f1212ba6facd162603">af658fbb</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-05-21T09:30:44+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed missing return value in cleanup_state.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/55c852fc17cd37a38751aa396644e7c62f94fb43">55c852fc</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-05-21T16:16:30+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Filename to RG ID header fix when merging, fix tab for space in merge tests
Fixes the fact that the -r option for samtools merge did not add entries to
the header.
Fixes the merge tests where a space accidentally crept in place of a tab in
test_input_1_b.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0e19c9e6ce0b432dc904a6a652ff497cf9a7e84b">0e19c9e6</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-05-26T13:15:34+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Change --outfile to --output; document faidx warning
Change dict --outfile to --output, as per the recommended long options
in the GNU Coding Standards.
Document the new faidx duplicate FASTA sequence warning (#380).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c2b423c629c905e3585aab26a814da63f1581b95">c2b423c6</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-05-26T13:17:33+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Reduce sam view usage fprintf calls
Create a multi-line string rather than calling fprintf dozens of times.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/99f2a2c4f1e98d2846a4ae4ff34f3915130c2d4a">99f2a2c4</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-05-26T13:47:48+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Further tweak samtools view usage display
Don't waste columns on indenting past "Options:".
Use C string pasting for the multi-line Notes string too.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7b346933a9df34c1c33799c98fb49604bbb2189a">7b346933</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-05-26T13:56:51+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge sam view usage code tweaks (PR #396)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/62d77118c35c7b1614b36567994a3297a3e175e6">62d77118</a></strong>
<div>
<span> by Joshua Randall </span> <i> at 2015-05-26T14:08:13+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Adds 'N' and 'Other' columns to `samtools stats` GCC output.
Fixes 376
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5e6d7bdbfbbc12d32328614fba99560895b161a4">5e6d7bdb</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-05-26T15:22:26+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update test data for htslib bin corrections
Update test_input_1_a.bam and [23].merge.expected.bam to have the
corrected bin values as per samtools/htslib#208.
Introduce a new test using "samtools index" to regenerate
test_input_1_a.bam.bai. This ensures that the .bai is newer than
the .bam; previously any commit that updated the .bam but not the .bai
(of which this would have been the first) would lead to test failures
due to "The index file is older than the data file" warnings.
Remove unused test_input_1_[bc].bam.bai indices.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/57320c5f962e3a76dc367cc0a438a10682bda31b">57320c5f</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-05-27T09:21:33+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Ignore "samtools depth" check outputs
(See also b94f0f2bc9c9b0e04c8a85b8673057a633d1b8df.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8b8ed6ae0561882f4a605eaff4bd3a83319c67e4">8b8ed6ae</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-05-27T11:52:11+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge 'N' and 'Other' stats columns (PR #397)
Modified to use a switch (jump table) rather than repeated if-stmts.
[NEWS]
* samtools stats now outputs separate "N" and "other" columns in the
ACGT content per cycle section (#376)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c18f0f59c84b8c343420713547984aec1709729f">c18f0f59</a></strong>
<div>
<span> by Petr Danecek </span> <i> at 2015-05-28T16:29:50+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>plot-bamstats: Remove hard-wired 60 columns fasta lines assumption
`plot-bamstats` with the `-r` option had a 60 columns assumption
about the fasta file which made for some strange looking lines
when run with GRCh38 for instance.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/23d901ec10bcf11ea87c35b93827fbc5240260b6">23d901ec</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-05-29T09:59:53+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Allow "cmd | samtools view" and write usage to stdout
Given just "samtools view", display the usage or view stdin (as per
"samtools view -") depending on whether the input is a terminal
similarly to other subcommands. This makes samtools view act more
like a typical Unix filter in pipelines. Hat tip @jwhsanger.
When it's not an error message (as in "samtools --help view" or just
"samtools view"), display the usage on stdout and exit successfully.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/42098f01a1ca6c3f09411bc8634e9b6bcb1177dc">42098f01</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-06-01T11:30:43+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>[man page] reorder as per incoming patch [minor]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1fe4b3c899ef9819686032431b6316ece7202c37">1fe4b3c8</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-06-01T16:58:59+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge man page additions (PR #381)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7802db38ee9ebfe73f9d1416eaa9c36fcfa83584">7802db38</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-06-02T14:08:12+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Samtools depad fixes (part 1).
Updated the bam header API to use htslib.
Fixed the test data for r051 so that it has the correctly depadded
cigar string.
Fixed the code such that it can now generate the correct output for
r051 too.
Changed the tests from expected fail to expected pass.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9c2461ea08a84ad8fb1fc38a05da2b5b16bf20b8">9c2461ea</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-06-02T17:34:41+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Switched to using htslib instead of bam.h. Plus CRAM support.
Also had to fix the test data to not have unmapped reads with a CIGAR
string as this isn't supported in CRAM. The change to stop this
blowing up in CRAM now also means that these strings do not get edited
in SAM or BAM either. I think that is valid though as they are
currently nonsensical.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/44e1a7491a35856139faeaf590178841f4845686">44e1a749</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-06-03T11:35:26+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge filename to RG-ID merge fixes (PR #394)
Hand-merged binary test data bin field fixes (cf 5e6d7bdbfbbc12d32328614fba99560895b161a4).
Dropped unrelated -s VALUE usage documentation complexification.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f85deba90bb9f4ccc265a10331155a51e782c2c7">f85deba9</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-06-03T14:38:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixes #201 - thanks Peter.
Merge complicated by the ancestry and that this all predates the grand
white-space unification. Joy!
Conflicts:
padding.c
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a03575bf50fdfd84359768be015d3fdf3d5063a6">a03575bf</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-06-03T15:21:08+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge branch 'develop' into depad
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e8044911d05a6bd738a164a665b73d3b939f03f0">e8044911</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-06-03T16:55:10+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added depad documentation.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/63c060d87d8e907d092ef8c71ada811b05e98367">63c060d8</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-06-03T17:55:24+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Further CRAM fixes.
CRAM output is now forced to using non-reference mode as clearly we
don't have a copy of depadded reference to compare against.
Also implemented the "TODO" comment. We now have proper @SQ parsing
and fixing.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8a0914e5208538c198ed17e8a1022998fca2b3c6">8a0914e5</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2015-06-10T16:08:30+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add checks for bam_hdr_read and sam_hdr_read returning NULL.
Also bam_header_read and sam_header_read which wrap the _hdr_read versions.
In main_bam2fq(), delay opening the singleton file until after sam_hdr_read
and bam_init1 have completed. This means it won't create an empty file
if either of them fail.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/93c45cc206af4f119758745d1c29c56d19a9d512">93c45cc2</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-06-12T14:51:23+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed #79
The reference is fetched during mpileup fetching/callback rather than
once processing a position, as the latter is too late to get the
correct ref seq for performing BAQ realignment.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/82002e6836c772b21a2816d71d7c7fe6c49d4d6d">82002e68</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-06-12T15:37:47+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed tests.
The tests were superficially manually checked to validate that the
differences are reasonable, but it's not feasible to accurately
calculate the impact of adding BAQ. ce#large_seq.bam now uses -B to
prevent excessive memory usage in realignment.
Also removed some commented out debugging.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5363823fae72b5de29c02d726002886b30c80eb0">5363823f</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-06-15T10:26:09+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Avoid using asprintf(), which isn't even a POSIX function
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a5f28a0f7a32c48ea7241913cec87fce0de35ab3">a5f28a0f</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-06-15T21:23:53+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge tag '1.2' into debian/unstable
Bug fix release
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/71af052b8ae35cb9ad1e1962c70b1d222e6e7937">71af052b</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-06-15T21:31:44+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream release ; no new copyright notice nor license term.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/712a2160145fbced8404adb8f54218f99da731e5">712a2160</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-06-15T21:43:54+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Corrected syntax.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/23e44a4110a57524a37a013e8eedf3bbc37c9541">23e44a41</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-06-15T21:44:28+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Removed fix_coverage_cap.patch, obsoleted by -d option.
See https://github.com/samtools/samtools/issues/284
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1091aab090d557e3891bf99e3d1271ffd852dc4c">1091aab0</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-06-15T21:48:58+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Refreshed fuzzy patches.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c542e84fd612419a7cf0f3caa1439c0870334d62">c542e84f</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-06-15T21:59:57+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Build-depend on libhts-dev 1.2.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c789e05419a795fa01a162aa84419f856d5385b8">c789e054</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-06-15T22:03:26+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Current changelog.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d2e84d56065aaee4842360f2e067ff5e3af8a2b0">d2e84d56</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-06-16T05:30:09+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Revert last commit, that included patched files by mistake.
This reverts commit c789e05419a795fa01a162aa84419f856d5385b8.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/affb220a30e7a4a3f31b43ecc801bcdca4b31d85">affb220a</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-06-16T05:30:38+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Current changelog.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e4c31091a774ee5b44f5b1d5f6c5e6b180a09796">e4c31091</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-06-16T06:58:56+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>samtools (1.2-1) unstable; urgency=medium
a5f28a0 Merge tag '1.2' into debian/unstable
c542e84 Build-depend on libhts-dev 1.2.
6c2d9cd Build-depend and recommend libio-pty-perl.
(Needed for the regression tests.)
23e44a4 Removed fix_coverage_cap.patch, obsoleted by -d option.
1091aab Refreshed fuzzy patches.
-- Charles Plessy <plessy@debian.org> Tue, 16 Jun 2015 06:12:12 +0900
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9bbc79ec8d793705007e2141c8f9483b39a4b397">9bbc79ec</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-06-16T12:18:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Report bam_index_build() errors via stderr and exit status
If bam_index_build() fails, print an error message and fail.
Finally completes fixes samtools/htslib#189, and fixes #362.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a717b05230db645d86dd697d05eeac504490c54d">a717b052</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-06-17T10:34:39+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge branch 'mpileup-segfault' of https://github.com/Debian/samtools into mpileup_BAQ
jkb: most of the changes in this pull request have been obsoleted by
the restructuring, but the core check still works. Thanks.
Conflicts:
bam_plcmd.c
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3b266baa1354e8b9911553db1d33220d5d70ab23">3b266baa</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-06-17T11:41:50+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Rewrite samtools reheader in terms of htslib API (instead of bam.h).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/29d6b58c0bb36c32dc30694a30564cbfb509b216">29d6b58c</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-06-18T10:34:52+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge depad improvements and conversion to htslib API (PR #404)
Update makefile dependencies and padding.c copyright years.
[NEWS]
* Samtools depad command now handles CIGAR N operators and accepts
CRAM files (#201, #404)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/39a35af020831e663614829c41b655ee7fa6f3ac">39a35af0</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-06-18T12:04:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge mpileup BAQ fixes (PR #407)
[NEWS]
* Samtools mpileup now applies BAQ calculations at all base positions,
regardless of which -l or -r options are used (previously with -l it was
not applied to the first few tens of bases of each chromosome, leading
to different mpileup results with -l vs. -r; #79, #125, #286, #407)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/160351cae2323c918d63070af5d41be238565934">160351ca</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-06-23T15:22:58+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Updated samtools reheader to work on CRAM.
There are now 3 modes:
1) BAM to stdout
2) CRAM to stdout
3) CRAM insitu.
Internally the insitu version is coded with a separate v2.1 and v3.0
CRAM implementation.
Also added tests for the above 3 cases (but not including the soon to
be outdated v2.1 support).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1500934cd8f80d41623db2f32bc7d036bade8b52">1500934c</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-06-24T17:06:18+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Updates based on pull request comments.
Insitu replace by in-place (and -I vs -i).
SAMTOOLS_VERSION replaced by samtools_version().
CRAM data struct manipulations replaced by an more officially
sanctioned external API in the new htslib/cram.h file.
Note: I haven't manually re-checked version 2.1 files yet. This
cannot be done via the test harness as it depends on the
output-fmt-option branch. I'll do this in a new PR.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a40932903ba4b1023f7b60e63a67873f3c7b6cd7">a4093290</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-06-25T15:08:54+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Check ref sequence length before examining ref base
Prevent fillmd (and other commands) seg faults due to reads with POS
invalidly beyond the end of RNAME. Hat tip @vvi.
[NEWS]
* Fixed calmd, targetcut, and potential mpileup segfaults when given broken
alignments with POS far beyond the end of their reference sequences.
* If you have source code using bam_md.c's bam_fillmd1_core(), bam_cap_mapQ(),
or bam_prob_realn_core() functions, note that these now take an additional
ref_len parameter. (The versions named without "_core" are unchanged.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/eca63aa1076f34f8fa0a536a7677e17a5fbb89ba">eca63aa1</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-06-26T09:24:45+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Without regions, default to 1..INT_MAX rather than 1..2^29
Fixes part 2 of #241 for depth and mpileup commands with no region
specified.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/66a968601567eefb4ccfa24897f8651b0c259e38">66a96860</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-06-26T15:49:45+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Revise stats to handle SECONDARY and SUPPLEMENTARY flagged reads properly
Break stats main down into smaller functions for readability.
Adjust stats to properly take into account secondary and supplementary reads
by adding code which turns on and off tests based on secondary and supplementary flags.
Add tests with supplementary reads.
Moved collect_original_stats code into it's own function based on feedback from pd3.
Signed-off-by: Martin O. Pollard <mp15@sanger.ac.uk>
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/26ddf378770049c02ab0bf2f04a97969c819d40d">26ddf378</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-07-01T14:27:52+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge stats supplementary/secondary fixes (PR #357; fixes #352)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9f0a46f9b81eaff980f2df29316e22766fe38a3d">9f0a46f9</a></strong>
<div>
<span> by Christopher Smowton </span> <i> at 2015-07-01T16:41:53+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Amend SAM header merge strategy to avoid two quadratic-cost operations and switch from expensive regexes to simple string.h operations.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a1814030f5a843e62619c61b3ffe857688e5d41e">a1814030</a></strong>
<div>
<span> by Christopher Smowton </span> <i> at 2015-07-01T16:44:08+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge branch 'develop' of https://github.com/samtools/samtools into header_merge_efficiency
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f845404614caaaf960e5219b0b7ad46b2b7d35c8">f8454046</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-07-02T11:41:10+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use vcf-miniview to bugfix the broken mpileup BCF test.
We don't use -f as it's good to have one test that checks everything
(and fix it if we knowingly break the test).
Fixes #410
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/cd323165f8b20601b25f257607bc24ac8e00cac6">cd323165</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-07-06T11:43:48+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove unused warning, update copyright years [minor]
Both are detritus from merge 26ddf378770049c02ab0bf2f04a97969c819d40d.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ddcde253f55b2b69bb3e8071b15a2248ac14ecef">ddcde253</a></strong>
<div>
<span> by Heng Li </span> <i> at 2015-07-07T02:17:42+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>allow to set the fraction of ambiguous bases
[Fixed typos.]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/86b0b1e56a611aa931fc632237112b7a9beabde9">86b0b1e5</a></strong>
<div>
<span> by Heng Li </span> <i> at 2015-07-07T02:17:42+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>bugfix: missing inserted allele in output
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9ab4379870b73aed58659cc829d3e89a68c06ac0">9ab43798</a></strong>
<div>
<span> by Heng Li </span> <i> at 2015-07-07T02:17:42+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>output contiguous deletion
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c19acd8040e94db7685360b65ed156dcbda5edc5">c19acd80</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-07-08T12:44:15+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixes #320 - fixed bug in bam_prob_realn_core with QUAL "*".
Also had to change the test files as the expected output has changed
(it's now sane).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/41044e3603bc6df34d0858fb436b5ada776167f0">41044e36</a></strong>
<div>
<span> by Peter Cock </span> <i> at 2015-07-08T14:43:41+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Describe output format in samtools depth usage string
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/66b2f5409bf9f0524ec9da98114f98e927d71298">66b2f540</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-07-08T14:49:35+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added synonym of -d max_depth to samtools depth for compatibility with
mpileup.
This also (sort of) fixes #322.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d8fab7acd5ae72c9d8d35bfbe9f8ea54864ac1ed">d8fab7ac</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-07-08T14:56:34+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge branch 'depth_usage' of https://github.com/peterjc/samtools into develop
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d968d4213efdddaf9ab847201e81e21f8c1c797c">d968d421</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-07-08T14:57:11+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge pull request #426 from peterjc/depth_usage
Describe output format in samtools depth usage string</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6f8478a70c52fac8bcd2c02fa12da848c9c3052c">6f8478a7</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-07-08T15:01:51+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge branch 'develop' of https://github.com/samtools/samtools into develop
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/877434b00eb0c531961bd8596999a5abcf0348e2">877434b0</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-07-08T15:06:15+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed accidental white space variation.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d9ff716b0d076318da55dc50ccfd112ff51e07de">d9ff716b</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-07-08T16:48:26+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixes #328
Whee, 7 months on and I'm assigned my own bug report. :-)
Samtools sort now returns non-zero exit status when it detects an
error, rather than message received, understood, and ignored!
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e72b2455362109a8264ce52311577f6034cf4eee">e72b2455</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-07-09T17:38:08+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed wgsim bugs.
Insertions on the reverse strand were being added by reverse
direction, so the sequence differed.
Insertions on the reverse strand were being added one base too early.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8f60492d1a81b362cf7630ee3ab8669fd21420e0">8f60492d</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-07-10T18:03:20+12:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Reactivate "samtools index bam bam.bai" command
Use sam_index_build2() added in samtools/htslib@e9b7db4474ee82fc33c883cc906985ec56b32802
to implement the 0.1.x two-filename index command. Fixes #199 and the
non-pass-through part of #427.
[NEWS]
* Samtools index's optional index output path argument works again (#199)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e2bb18fe234a1d3000d562016e9531e2e224f2d9">e2bb18fe</a></strong>
<div>
<span> by Sam Nicholls </span> <i> at 2015-07-17T16:48:40+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add support for multiple file comparison in tests.
* Add `out_map` hash to test_cmd args hash. Keys are the names of
expected output files which map to the path of the expected output
of that particular output.
* Add `hskip` to test_cmd args hash. An integer used to splice out
the desired number of lines from the head when reading the actual
output file in to the `$out` array, allowing for a match to `$exp`.
* `out_map` does not override or intefere with the `out` argument and
can also be used alongside it to check both stdout and multiple
expected output files.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7584cf6f6c0acebd1f0b9e8f11fba068d6feeb6b">7584cf6f</a></strong>
<div>
<span> by Sam Nicholls </span> <i> at 2015-07-20T11:25:10+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Allow splitting of statistics on tags
* Removed several 'global' statistics parameters such as
`cov_[min|max|step]`, `gcd_bin_size` to a new struct: `stats_info_t`.
* Each `stats_t` holds pointer to `stats_info_t` to avoid passing the
info structure around to every function that needs access to the
user specified "global" options.
* `output_stats` accepts new first parameter for target FILE*.
* New `init_structures` function accepts a `stats_t` and initialises it.
* `split_hash` khash structure maps RG IDs to an address in memory
corresponding to a `stats_t` for that particular read group.
* New `split_stats` accepts a `stats_t` and `split_hash` and creates a
new `stats_t`, inserting its address in to the hash.
* `all_stats` maintains old behaviour and is written to stdout.
* Other `stats_t` are written to files in the format <bam_fname>_<RG ID>.bamstat
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/09cf53cba44a3d1e8c6b5350f23ad6147d49bb77">09cf53cb</a></strong>
<div>
<span> by Sam Nicholls </span> <i> at 2015-07-21T10:30:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use stats_t* over intptr_t in hash
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/227c142c288b4757e9bd7907a0b52a9f16ee451b">227c142c</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-07-28T16:21:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix for -c and -p in merge and sort
-Add fix so that -c and -p put the first @RG or @PG into the output
-Add testcase to check the -c and -p
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ad1c71e2f32da597ea01980375eebfa13535389a">ad1c71e2</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-07-29T10:39:05+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Avoid filenames containing colons, which are invalid on Windows
Windows dislikes <>:"/\|?* in filenames, and colons interact somewhat
oddly with Mac OS X's Finder (which displays them as slashes).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/784b4f53eb769d25e0b0774857106622038745e1">784b4f53</a></strong>
<div>
<span> by peterjc </span> <i> at 2015-07-29T11:48:50+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>samtools depth usage typo and longer line wrapping
Fixes my typo (repeated 'the') and makes the usage text line wrapping
use longer lines.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/598f4a0f1dd9185e7e5b686e6beaf981465e1799">598f4a0f</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-07-29T13:20:43+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Replace xz-compressed test data file with gzipped equivalent
Avoid xz, which may not be installed by default especially on OS X
or Windows. To improve gzip compression of this data, we only gzip the
interesting fields and reconstruct chromosome/position in fields 1 and 2,
reducing the gzipped data from 3M to 582K -- hat tip @jkbonfield.
(The doubled \\ escapes the backslash from sh(1)'s read builtin.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/04ca94363a0d3d22d0aba16c028eb7a118ee0f7e">04ca9436</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-07-29T16:09:12+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Enable travis OS X to test cross platform bugs
-Enable travis "osx" platform
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/09095862ee534ab4bb054d87d0927752d369cd86">09095862</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-07-31T15:16:59+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge reheader support for CRAM files (PR #412)
Updated bam_reheader.o dependencies, added *.tmp.* temporary test file
cleaning and renamed new tmp test files, completed s/in situ/in-place/g.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6d6208ad41afc3b566eded7983acb8bc647c60f2">6d6208ad</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-07-31T15:36:01+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed the mpileup test to avoid floating point 32/64 bit issues.
It's a hack as we chop off the last digit rather than rounding
correctly, but it happens to be sufficient for the test data we
currently have. If we later get data that rounds from say 0.9 to 1.0
then we can rewrite it with a bit more cleverness.
Fixes #445
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a63070c05aa7a09b0ba02c2e7776366524c8d5b2">a63070c0</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-07-31T15:38:35+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added input/output-fmt-option to man page.
[Moved added section to before REFERENCE SEQUENCES; fixed typos and
improved formatting -- JM.]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/75ae6d4d0fdfb80504e0cd2c4a6c02d54c4ed9b9">75ae6d4d</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-07-31T15:40:36+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge branch 'develop' of github.com:samtools/samtools into develop
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/26f57e3ab0f4b9b0344b5e6bde4693b069decb25">26f57e3a</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-03T10:44:37+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use POSIX awk gsub() rather than GNU gensub()
For example, some Travis build hosts don't have GNU Awk.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1278126df2a9422fbde53abee6d2606f89d261b4">1278126d</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-03T13:31:55+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Preserve TAB characters in command to be executed
Current dash (and apparently whatever bash version travis-osx uses)
read -r translates \t etc escapes into control characters. Ensure
that these survive intact rather than evaporating into spaces: for
uses like "awk -v OFS='<tab>'" the difference is crucial.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1669c256db4dfc07891f571c524acea6dac89c72">1669c256</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-03T13:46:35+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge FP last digit removal filter (#445)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5812c9b6e9f3a6af3a4f26c00c6e6227d4db1753">5812c9b6</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-08-04T10:43:46+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add facility to escape regex inputs
Add regex_escape to escape extended regex meta chars.
Add regex_escape calls to ID fields embedded into regex searches.
Add testcase to demonstrate that this fixes #434 and fixes #409.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/999def39e28a267c87ed173e9d1827524e9864b4">999def39</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-04T12:09:37+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Properly preserve \t and other escape sequences
The problem apparently down to dash's read -r was in fact caused by its
echo builtin translating \t etc. Echo is not portable w.r.t. whether
it parses backslash-escapes or not; fix this properly by using printf(1)
instead.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b8ff342fd5846c5df6129d67b154aa8c1a157d8f">b8ff342f</a></strong>
<div>
<span> by Martin Pollard </span> <i> at 2015-08-04T13:32:33+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Misc code cleanups
Replace != with < in for loops in errmod.
Replace 0's with NULL in bam_plcmd.c
Replace exit(1)'s with exit(EXIT_FAILURE)'s in bam_plcmd.c.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d1d3cd2d7c1585a700fd081fa8f5dc9834aa6c14">d1d3cd2d</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-05T09:17:34+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Minor sam_opts updates
Constify several parameters, avoid arbitrary length limit in "reference=%s"
construction, change include guard to match filename.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/78c23438066eb38fd6e04924559ae6db32cef9b0">78c23438</a></strong>
<div>
<span> by Shane McCarthy </span> <i> at 2015-08-05T14:47:12+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>mpileup output updates for VCF4.3
* the unseen allele is to be specified as <*> rather then X or <X>
as has been the case in mpileup for a while.
See samtools/hts-specs@4a917457cb9be262bbe22634a90ece2e0dd08f48
Note that bcftools call supports X, <X> and <*>,
see samtools/bcftools@802ff309822b8648cc3b7022e3a72e3312e03279
* add options to output AD,ADF,ADR (samtools/hts-specs#78)
* deprecate DV,DP4,DPR annotations as largely superseded by
the new AD tags
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4bf18861623e6268e4e29b900c3bfa2964fa0dea">4bf18861</a></strong>
<div>
<span> by Shane McCarthy </span> <i> at 2015-08-05T15:11:19+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>resolve merge conflict
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c03fec6c5dde1542f0279b9bde7bd97e8407d216">c03fec6c</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-06T11:32:26+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Replace assign_short_opts() so struct options can be const
Use the new SAM_OPT_GLOBAL_OPTIONS() to const-initialise the various
struct option lists correctly, so we don't need assign_short_opts()
any more.
For subcommands which have their own additional long options,
assign_short_opts() left incorrect entries behind as it did not shift
all entries when disabling options. Instead we mark disabled options
with '?', so that they are parsed and return '?' from getopt_long(),
signalling a usage display. (It remains to verify that all subcommands
treat '?' appropriately.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/32fd3af9b0177c006d90c995bb906892d2b7746a">32fd3af9</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-06T15:14:03+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Actually test multithreaded Big SAM -> CRAM
(Aaaaaaargh!)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9951654ee851365cfb1dedd1cb967ac68f114b0d">9951654e</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2015-08-07T17:40:11+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge pull request samtools#436 into branch for samtools#419
Also fixed tabs that came in with samtools#419.
Conflicts:
bam_sort.c
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4dda6177450c2ed88f7bb7d9ecaa7bf11b077962">4dda6177</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2015-08-10T12:09:03+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Make test_trans_tbl_init build and run successfully.
Pass target names hash to trans_tbl_init().
Update setup_test_* functions to initialise the hash with the pre-existing
target names.
Add some printfs to make it easier to find out which tests passed/failed.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/71e1a62defc59ed4c71f281b68e259325ed6f791">71e1a62d</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-10T15:52:43+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Finish cut_target.c conversion to htslib API
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f78373cbda8f6a2406a345fbbb02f6d374a9984e">f78373cb</a></strong>
<div>
<span> by Sam Nicholls </span> <i> at 2015-08-10T23:59:44+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>`samtools sort` usage [Fixes #418,#356,#349,#295]
* Removes checking for modern or legacy usage and assumes all usage
follows modern syntax.
* `-T` is no longer required and is set to <in.bam>.tmp.NNNN.bam by default.
* Without `-O`, output format inferred from input with sam_open_mode. For
stdin, bam output is assumed unless specified.
* Updates samtools.1 and bam_sort.c usage syntax.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/998188a6564d18eb23e74ccfab50e473fd03e50f">998188a6</a></strong>
<div>
<span> by Joshua Randall </span> <i> at 2015-08-11T10:14:39+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Adds `samtools quickcheck` subcommand
`samtools quickcheck` opens a set of SAM/BAM/CRAM files and
checks that the header of each contains at least one target
sequence, then (currently for BAM files only due to htslib
API limitations) seeks to the end of the file to check
whether the EOF block is intact.
Exits with a zero status if all input files checked out ok,
or a non-zero status otherwise. Can be made to give a list
of failing files (on stdout) using the `-v` option or to be
more verbose (on stderr) by giving additional `v` options.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b1a5854518649e665f8abba97d42f17e28b1bad9">b1a58545</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-13T16:43:36+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge --output-fmt-option etc global option handling (PR #395)
Consistently constify bam_tview*.c's *_tv_init() fmt parameters.
Similarly in bam_split.c and bam_sort.c.
Change bam_split.c's %f to %. (similar to the existing punctuation-based
expansions and to other similar tools), and document the added % expansion.
Restore bam_sort.c's bam_merge_core() and bam_sort_core(), which are
potentially used by legacy third-party code.
Add $(sam_opts_h) dependencies, and fix miscellaneous dependencies.
Call sam_global_opt_help() in bam_plcmd.c, bam_tview.c, and cut_target.c.
Fix bedcov.c and sam_view.c usage displays. Fix bam_plcmd.c, bam_stat.c,
and sam_view.c option error handling.
Fix bam2depth.c usage message typos (hat tip @velcrospud).
Correct sam_opts.c whitespace.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8853bc6bde2dd6be1582f2241079c91b64f4f179">8853bc6b</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-13T16:55:39+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix FILE* destination for usage output
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b3fb0f29cdfccfedc794d027de6be9795f5e27c0">b3fb0f29</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-13T17:11:43+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Improve man page table formatting [minor]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f246dbc60c1b308a818ad11ec550e39bc8bebc3e">f246dbc6</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-14T09:22:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix stats.c memset() thinko
Fixes segfault whenever realloc_buffers() is called. Hat tip @vvi.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f282777b43abf01961e2d32ef3bb60758e86dafc">f282777b</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-14T12:52:55+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add quickcheck subcommand (PR #406)
Added Makefile dependencies and test/test.pl tests.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4054ba5fd0c69ba55ae61e725543f38f5a26e320">4054ba5f</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-14T13:59:16+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Reformat main samtools usage display
More whitespace, and a wider subcommand name column as there are
some longer subcommand names approaching.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ab561e1c8369836a224658118b4ceaddabaa601d">ab561e1c</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-14T16:46:33+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add accidentally omitted short option [minor]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/858b0e7c73494d9273e23c41c2ec8628a9fd85df">858b0e7c</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2015-08-17T09:56:17+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Improve header merging.
Add new merged_header_t struct to store state for the combined output
header. This is passed in to trans_tbl_init instead of a bam_hdr_t. It
includes hash tables which allow the presence of a @SQ SN, or @RG or @PG
ID in the output to be rapidly tested. It also includes separate kstrings
for the various record types, which makes it easier to get the desired
ordering of records in the combined header.
The monolithic trans_tbl_init function is broken up into smaller parts that
handle the different record types, and rewritten to use the new
merged_header_t struct. A couple of combined functions deal with the RG
and PG records, eliminating some duplicated code.
pretty_header, regex_escape and copy_headers are removed as they are no
longer needed.
New functions init_merged_header and free_merged_header are added to create
and tear doen the merged_header_t struct, along with finish_merged_header
which creates a bam_hdr_t from the data in the merged_header_t. This
effectively replaces pretty_header.
bam_translate prints warnings to stderr about tags that do not appear in
the header. It now tracks which ones it has warned about so it only
prints one message for each combination of ID and input file.
test_trans_tbl_init.c is modified to work with the new merged_header_t
struct. A lot of duplicated code is also eliminated, especially from
the setup_test_ functions.
As pretty_header has gone, test_pretty_header is no longer needed and also
removed.
test/merge/3.merge.expected.err is changed to reflect the changed
warning message from bam_translate.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d946f49bd638679167c6d91e9acf308ff785b3ac">d946f49b</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-17T10:44:59+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Reheader: added explicit version 2.1 and 3.0 cram tests as the code
has specific functions for each version.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/28772779f1e6254ee291babaedda1738cee0ab63">28772779</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-17T10:53:30+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Improved test harness to report the errors
...produced when a command fails to run. Otherwise it's very hard
to tell why a Travis build didn't work unless we can reproduce it.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3c2003eaa90228746e40c94525b7323c0fbe8634">3c2003ea</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-17T10:57:48+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge separate CRAM v2.1 and v3.0 reheader tests
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/49ed75498f78d2fc782afc8964af7ecca2bf60e3">49ed7549</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-17T11:13:14+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Made samtools cat work, when possible, with CRAM files.
The cram variant is subtly different in that where possible it
reconstructs the joint header by stitching the @RG lines from the
concatenated files, but the -h option is still available.
Changed it so it works with 1 file. It's a bit esoteric, but
technically there is no reason why it requires 2. (Unix cat copes
with 1 just fine.)
Also fixed a small memory leak in reheader.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8a7a1e7d67d049d409b711bc1e5026fa434aebf4">8a7a1e7d</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-17T11:13:14+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed samtools cat crash when given invalid filenames.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9f4d3610af3b7c82c96e9b0ef4a91464a4633e8c">9f4d3610</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-17T11:13:14+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added CRAM tests for samtools cat.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7ba7dc32afe4a1ec1ded25b7a4870b64f13a32a4">7ba7dc32</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-17T16:55:41+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use hts_get_format() accessor function
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/08df3db1b860b4b67a076a845bbc4b722b044fc3">08df3db1</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-17T17:08:27+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge samtools cat for CRAM files (PR #420, #451)
Updated bam_cat.o dependencies.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/719060704f187124aab3691ba03a23356836ce2f">71906070</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2015-08-18T09:34:26+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Replace regex searches with dedicated match function.
Glibc's regexec calls strlen, which makes it very slow on long inputs.
Replacing it with a function that only inspects the parts of the input
text that it needs to gives a big speed-up for large headers.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/226cb15ecd39d262b4a7f9d609a96de07cff2159">226cb15e</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2015-08-18T11:40:02+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Deal with out of order @SQ lines.
@SQ lines should really be in the same order as the entries in the
binary header. Instead of adding them each time a new one is found,
record the position and add the lines in the same order as that in the
binary header at the end. This ensures the ordering even if the input
files are incorrect.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5edde1e2f7ca40b957d942138748083dd92df251">5edde1e2</a></strong>
<div>
<span> by Shane McCarthy </span> <i> at 2015-08-18T12:22:54+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>skip first bin for AD and DPR calculations as this stores the totals for the site
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0c5617ecd9c3930024bfcec02ac0796c1abfbd67">0c5617ec</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-18T14:21:43+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge mpileup updates for VCF v4.3 (PR #448)
[NEWS]
* The mpileup command now outputs the unseen allele in VCF/BCF as <*>
rather than X or <X> as previously, and now has AD, ADF, ADR, INFO/AD,
INFO/ADF, INFO/ADR --output-tags annotations that largely supersede
the existing DV, DP4, DPR annotations
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/df82d58a756bf2a2cb688d30702cea9dbf26da4e">df82d58a</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-20T08:43:25+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Rename hash to c2stats to reflect previous intptr->stat_t* [minor]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e55418f89f0d0b3a348f0e32ea5cf0e33f29896b">e55418f8</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-20T10:09:05+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Prefix errors with "samtools <subcmd>:" rather than "samtools:"
When several samtools commands are being piped into each other,
this improves the chance of knowing which one is complaining.
Also flush stdout (stderr) before (afterwards) as recommended by
https://utcc.utoronto.ca/~cks/space/blog/programming/HowToWriteToStderr
This makes a real difference in the "samtools foo >out 2>&1" case.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/dce3c288c3e31249a0183c52d489cad42c74a78d">dce3c288</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-20T13:32:47+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge header merge non-regex-based rewrite (PR #453)
Finish removal of test_pretty_header.
[NEWS]
* Merging files with millions of headers now completes in a reasonable
amount of time (#337, #373, #419, #453; thanks to Nathan Weeks,
Chris Smowton, Martin Pollard, Rob Davies)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8be7f04b3b1793a70eaf17aac10793b1e532d1e8">8be7f04b</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-21T10:15:42+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge James's wgsim bug fixes
Bump version number to 0.3.2, beyond any wgsim version number in this
samtools repository or in github.com/lh3/wgsim.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8e3e23f82d7bde2636b7b9eb591ec32197d95843">8e3e23f8</a></strong>
<div>
<span> by Kevin Murray </span> <i> at 2015-08-21T10:27:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add manpage for wgsim
Fixed man page typo. Updated copyright to match source.
Tidied up .TH. Removed version numbers from this simple man page,
so there's one less place to update with releases.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d779e259d4b14743195ed0a0a14d7ac6c4d7ad1a">d779e259</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-21T10:33:35+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merged wgsim_eval.pl with
https://github.com/lh3/wgsim/commits/master/wgsim_eval.pl
(Author: lh3, but no common git history to work on.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4bfd61182c649acd0ab3ded7717d41f9ab37a842">4bfd6118</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-21T10:33:36+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added some help to wgsim alneval.
Feel free to add documentation of -c. It was in the original code, but
silently removed in a later revision (by Heng)? I left it in during
merging but aren't sure what it does. So it's undocumented and hidden
for now; left in for compatibility only.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8e9b6f956a84abbadce530eeb66e75b571a3250b">8e9b6f95</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-21T10:33:36+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Tidied up white space to be consistent across entire file.
(It's not consistent with all other perl scripts here because there is
no consistency between them.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7e4b541ce8d2b4a02422142853d1a8a6f2229f33">7e4b541c</a></strong>
<div>
<span> by Karel Brinda </span> <i> at 2015-08-21T10:40:16+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Support for X and = in CIGAR strings
[Cherry-picked PR lh3/wgsim#6.]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ea5a92f74e339eae0ea8fcbcb0109f7bae27c3dc">ea5a92f7</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-21T10:50:31+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge misc/wgsim updates and man page (PR #428)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/881e2249f8c9bd97aa53d02a6826015fcbcae55e">881e2249</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-24T10:22:13+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Rename split option -T/--tag-split to -S/--split
Add samtools.1 documentation, and remove -s/--sam documentation (input
format is always auto-detected). Simplify split_tag option handling.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f0cb72c73c6ed47d6ee305ade2d18feb3aac7ca8">f0cb72c7</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-08-24T11:19:13+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Split out bam1_t to fastq processing and add option to output to files.
Add -1 and -2 options to output FASTQ to files instead of STDOUT.
Separate out bam1_t to fastq processing step and make it self contained.
Add options to filter reads by flags.
Signed-off-by: Martin O. Pollard <mp15@sanger.ac.uk>
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/289ae950fbbeab3cd8de73c53501a354460952dd">289ae950</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-08-24T11:19:27+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Comments to explain bam2fq mainloop
Add some comments to explain two stage output of main loop.
Signed-off-by: Martin O. Pollard <mp15@sanger.ac.uk>
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/20b5b13d04482e48dab93f5bc7ff1c57a825de86">20b5b13d</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-08-24T12:53:33+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Refactor bam2fq arg parsing and init
Move argument parsing for bam2fq out of main.
Move state initialisation for bam2fq out of main.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e762eec610095fb7d826fb35f2360236541242c2">e762eec6</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-08-24T12:58:23+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add comments to bam2fq mainloop
Add comments to bamtofastq mainloop.
Convert readpart to enum
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/50ad1b5416775f5b0299819b64957351e0c6e72c">50ad1b54</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-08-24T13:07:36+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Rewrite branch 'bam2fq_format' of github.com:peterjc/samtools into bam2fq_improve
Don't mix FASTQ and FASTA in output.
Add default quality where reads don't have quality.
Reimplemented to fit into current bam2fq working branch. Hat-tip to Peter J Cock for original.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/dbea849772b863ad775e7b8eb7826f75dc5f3e51">dbea8497</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-24T15:41:05+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge samtools stats splitting (PR #421)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8d792d2f83310ccb77b5bc5150e2db5ca5f3fc24">8d792d2f</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-25T09:21:43+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Inverse video mode for tview and also changed some colours.
Fixes #457
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1849a6ec0e9863e64d4fd9cb1d3d91889d9a2d86">1849a6ec</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-25T10:07:21+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed wgsim so that it doesn't have infinite loops if it finds a sequence of Ns.
Sorry about the use of goto, but I find it clearer than reversing the
incrementer phase so the for loop inc becomes a nop; especially now it
needs a reset of max_loop.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b73d36e9281a9c23829f0cee22f9a9af184d1899">b73d36e9</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-08-25T10:19:55+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Rewrite of bam2fq singleton tracking with tests
Squashed several abortive attempts into this commit for a simplified merge
Rewrite singleton tracking into simpler form based on John Marshall's pseudo code
Add tests to new bam2fq codepaths
Add test to -1 and -2 options for bam2fq.
Fix fclose return value stupidity
Add tests to exercise the BAM_FSECONDARY|BAM_FSUPPLEMENTARY code paths
Changed double pointer of fpr to array of 3 pointers.
Changed r0,r1,r2 into an array of 3 pointers.
Reordered and tweaked usage message to match up with new style.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6a22b4f347369c09d0bf9d35e9e7813e78e271fc">6a22b4f3</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-08-25T10:23:16+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Rename bam2fq to fastq and fasta respectively
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3c0e3a5a5f2445722140215ae977eb16da0436f5">3c0e3a5a</a></strong>
<div>
<span> by Sam Nicholls </span> <i> at 2015-08-25T11:52:30+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add stats split prefix support and split indicator
* Add `-P`, `--split-prefix` to `samtools stats` to prepend
filenames created by `-S` or `--split` with a path or string.
* Add an additional comment line at the head of `samtools stats`
output to clarify whether the statistics pertain to all or
a tagged subset of reads.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f75eb347b1ca63afe0092fc31c50580346ba54c1">f75eb347</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-25T12:24:51+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Calmd now accpets the global I/O options.
Note that this is largely pointless on CRAM except for the unlikely
case of a CRAM file built with the no_ref option.
Also fixed a crash when the specified reference file cannot be
loaded.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8123d02180c09b408922c5e244acd17b90eaed0f">8123d021</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-25T14:21:20+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Minimal fix to make --reference replace -f fasta_ref when not
explicitly specified.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/55203720cddb64cb3a68dfeffcc1d4ed14bfb28f">55203720</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-25T14:30:23+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Tview now uses --reference value if specified (and ref not manually specified)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/77761c371e4f354cc635e22110131bb398b39f31">77761c37</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-25T14:35:51+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added depad to help output.
I think we fixed the bugs, so I don't believe it's any more unstable
than other tools. Plus it's in the man page already.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/cf18e41465aefb1841952a5c768f234460de476b">cf18e414</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-25T17:28:57+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added global i/o options to "samtools depad".
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3ab5f6c446897af8d016dd7f4a59ddcb0b098e52">3ab5f6c4</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-26T12:25:48+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Made targetcut -f and --reference the same option.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8f3e729bc5236d9179d5d63fbb93a68c1f6e0fd4">8f3e729b</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-26T13:41:41+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Have stats --split-prefix set the output prefix rather than adding to it
Previously "samtools stats -P foo/bar -S RG data/seq.bam" would try to
write to foo/bardata/seq.bam_<rg>.bamstat, and likely collapse because
foo/bardata doesn't exist. Better if we write to foo/bar_<rg>.bamstat as
that doesn't involve any directories not obviously specified by the user.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3e9357c36a34f21f103c1d5195682142ab3cbc15">3e9357c3</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-26T13:53:56+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge stats split output filename prefix (PR #460)
Alphabetised man page and usage options.
Fix misc/wgsim.c whitespace [trivial].
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/13de48f8dd6bcd71277128143fadc9ab3aa50576">13de48f8</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-26T16:21:00+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added a bam_get_library() implementation.
Needed by rmdup and view. Also resolves 6 of our expected failures.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/fff21fe564679684b18db17ce90c0ed96469a9ae">fff21fe5</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-26T16:25:19+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Updated the rmdup command to use the newer htslib interface instead of
the old bam.h one.
Also added the new I/O long-options.
Finally, due to the previous addition of bam_get_library(), this is
now "working" for the first time since 0.1.x series.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/77c8b4e57da6b9fba561ecf0e828bbdc2e99af22">77c8b4e5</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-26T16:45:15+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added recently changed #include dependencies to Makefile.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/25bee0e1d4dbb23a4885bb659bbbeb205e6c31d4">25bee0e1</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-08-26T17:55:15+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added calls to sam_open_mode() to auto-detect file format by name.
This fixes the output for fixmate, rmdup, merge, sort and depad. Note
it does not change the behaviour of samtools view -o FILE as I believe
this didn't previously auto-detect format, but it's trivial to add
that too if required.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5b3280d27de3802e8d33fa2507bb1efc46dce0f4">5b3280d2</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-08-27T23:58:59+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Document make targets to build htslib utilities
$(HTSDIR)/htslib.mk now supplies both all-htslib and install-htslib
targets. Fixes #462.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2bd7837fd0f3ffaa5a19a5d5dddcd54884b7ee6c">2bd7837f</a></strong>
<div>
<span> by Sam Nicholls </span> <i> at 2015-08-28T16:16:44+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update stats --split-prefix usage to match 8f3e729</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4d2efe9320ab25bd9dfba21acd2f5c59356e6cdd">4d2efe93</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-09-01T13:44:31+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use kstring's kgetline()
[stats.c] Remove mygetline() in favour of kgetline(). Closes #383.
[test/**.c] Use kgetline() instead of getline(). Fixes #392.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/fcaafe04ca155dd0517d49cde7e5f6722d878f76">fcaafe04</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-09-01T17:39:18+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge pull request #459 from samtools/tview_colours
Inverse video mode for tview and also changed some colours.</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/11ccd2a328420db592af01c5a110e0e9a3de6173">11ccd2a3</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-09-04T11:43:51+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added -o/-U filename.<suffix> detection to samtools view.
Also fixed a bug where using -C and -U together failed due to not
specifying the reference to the -U cram file.
The suffix used can differ between -o and -U. The format is
overridden by -b / -c or --output-fmt. It is not possible to specify
a different format for -o and -U except via suffix guessing (this was
not possible previously either as there is only a single -b/u/C
option).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/495b86cd941d91eb46b0ef7b311979cb57320a9f">495b86cd</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-09-07T13:15:54+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add missing Makefile dependencies
Remove bam_pileup.o, which was removed in e7ae7f96c7e78a2dd6eabdaed57037c483951929.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/093192e2afcca6ec8c800135aa9d0529bf148638">093192e2</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-09-07T13:23:11+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Canonicalise Makefile dependencies [minor]
Reorder prerequisites to the same order as #include lines in the source
file, which facilitates automatically generating these dependencies.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3978ecaefed6248996e342fe035c367348491c17">3978ecae</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-09-07T13:30:09+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixup bam2fq true and false, update copyright dates and man page.
Man page had old command names on it, update them.
Make true success and false failure for our functions.
Update copyright dates on test SAM because changes core to what
they're about were made when these derived works were created.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/af76b1ae39e5a2240f514aee0723bd48b05d1ea9">af76b1ae</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-09-08T16:23:12+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Reformat calmd_usage() to 2-space option indentation
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/caea801663cc127443a5a82b3b5c4c382345ca30">caea8016</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-09-09T17:26:00+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge --output-fmt-option etc followup (PR #461)
Update copyright years in bam.c, bam_rmdup.c, bam_rmdupse.c.
Use HTSlib's bam_endpos() instead of bam_calend() in bam_rmdupse.c.
[NEWS]
* The rmdup command no longer immediately aborts (previously it always
aborted with "bam_get_library() not yet implemented"), but remains
not recommended for most use [#159, #252, #291, #393]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e0306d254c8f8b30f273090323a72d070ff0659d">e0306d25</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-09-11T09:09:29+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Port addreplacerg command over from separate repo
Port command to add or replace readgroups in BAM/CRAM over from standalone repository.
Signed-off-by: Martin O. Pollard <mp15@sanger.ac.uk>
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0bd5498c08926b4fcc09b6256d2218eb100f857d">0bd5498c</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-09-11T09:09:30+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add ability to add new RG to file.
Rework command line options.
Allow choice between overwriting all tags or only those where no
existing RG tag exists.
Signed-off-by: Martin O. Pollard <mp15@sanger.ac.uk>
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/74b4c594d06b007ee805b36fce02831b5b377b69">74b4c594</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-09-11T09:09:30+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add long input and output format options to addreplacerg
-Adapt code to use new input/output formating options
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9a8f2f6d8a02c2052319b7a5c9c920ba14e5fffb">9a8f2f6d</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-09-11T09:09:36+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixes for addrprg based on @jmarshall's review
Fix man page.
Const init param pointer.
Do not unescape \n's.
Remove old mode format craft.
Convert to more conventional readloop.
Add alternate -r syntax.
Tweak documentation for addreplacerp.
By default write to stdout and add a -o option.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/798c7bc6905f4208321d1defbfbea93b9e690568">798c7bc6</a></strong>
<div>
<span> by Sam Nicholls </span> <i> at 2015-09-11T09:09:36+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Correct stated default mode for addreplacerg
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/93973873441f03960bdadaef2b66947472b87721">93973873</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-09-11T09:09:37+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>addreplacerg style fixes, usage correction and bugfix
Fix where in file was being set by the -o option.
Update usage to add -o
Update man page to change input.srt.bam to input.bam
Fix memory leak in parse_opts
Update to new print_error_errno syntax
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/17a8d7908d3236a15e8a137f69298859a0684e00">17a8d790</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-09-11T13:21:52+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix addrprg entertaining off by one error, spec valid but breaks stuff
l_text in header according to the spec can include '\0' however this breaks some parsers.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2f148b1560fdf1f6df1cb6fd467e9f81670a7df1">2f148b15</a></strong>
<div>
<span> by Afif Elghraoui </span> <i> at 2015-09-13T18:49:19-07:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Set up a new changelog entry
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/eb56918001cda9174a4d7078d91d171e158772d7">eb569180</a></strong>
<div>
<span> by Afif Elghraoui </span> <i> at 2015-09-13T18:51:50-07:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add patch to fix building on i386
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/702d28926f97b3acb9ce92705cbbe28b41015615">702d2892</a></strong>
<div>
<span> by Afif Elghraoui </span> <i> at 2015-09-13T21:08:18-07:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove source files not present in upstream tarball
I'm not sure how they got there, but they cause problems
when building the package.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7afd302dc02a8c4521017b68a3db4063ff86c4ac">7afd302d</a></strong>
<div>
<span> by Afif Elghraoui </span> <i> at 2015-09-13T22:19:17-07:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Allow all scripts to be called without language extensions
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c6cefd5c59c2f1ea3e69bd83570adb103a11ea35">c6cefd5c</a></strong>
<div>
<span> by Afif Elghraoui </span> <i> at 2015-09-13T22:22:04-07:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update changelog for 1.2-2 release
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c76e08da944a26ffd7867bf0a47ff40802d6f0bf">c76e08da</a></strong>
<div>
<span> by Afif Elghraoui </span> <i> at 2015-09-13T22:29:26-07:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Mark release and remove redundant changelog entry
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7c4cce46a0f29aac0182f7d4210b593389eed34e">7c4cce46</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-09-15T15:46:01+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add addreplacerg command (PR #371)
[NEWS]
* New addreplacerg command that adds or alters @RG headers and RG:Z record tags
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c740a12b1a8f3fde3f4878f1c1067c40e05f7c24">c740a12b</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-09-16T18:02:31+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Revert "Remove source files not present in upstream tarball"
This reverts commit 702d28926f97b3acb9ce92705cbbe28b41015615.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/876f680fec0be152a7175764ed4920ce0dcc8307">876f680f</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-09-17T20:18:41+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Note that this source package is managed like htslib.
This message should point to the Debian Med Policy once it is updated.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6691fed22acb37d156000f4c6b699a03ccbfd714">6691fed2</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-09-17T20:23:10+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>samtools (1.2-2) unstable; urgency=medium
[ Afif Elghraoui ]
eb56918 Add patch to fix building on i386
702d289 Remove source files not present in upstream tarball
7afd302 Allow all scripts to be called without language extensions
[ Charles Plessy ]
876f680 Document the update workflow of the source package's repository.
-- Charles Plessy <plessy@debian.org> Thu, 17 Sep 2015 20:21:15 +0900
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/dffc67f33e6534acb96c6fea08675d5b7ce9b0f9">dffc67f3</a></strong>
<div>
<span> by Benjamin Schuster-Boeckler </span> <i> at 2015-09-17T15:17:31+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added code to fix #343, thanks @cyrusmaher for the pointer in the right direction
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/19de55eeac5cc4f635720eb857f427ba091237d7">19de55ee</a></strong>
<div>
<span> by Afif Elghraoui </span> <i> at 2015-09-22T06:39:58-07:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Revert "Allow all scripts to be called without language extensions"
This reverts commit 7afd302dc02a8c4521017b68a3db4063ff86c4ac.
Closes: #799698
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/658179c6e1ac91d3f71882f7653f72d3f93c95b9">658179c6</a></strong>
<div>
<span> by Afif Elghraoui </span> <i> at 2015-09-22T06:41:10-07:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Revert "Remove source files not present in upstream tarball"
This reverts commit 702d28926f97b3acb9ce92705cbbe28b41015615.
This does not really cause a major problem.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0662664019ce89ac0e09315767b22a688f5ff96e">06626640</a></strong>
<div>
<span> by Afif Elghraoui </span> <i> at 2015-09-22T06:54:59-07:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Prepare for upload
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/32bbc4518877052c5ec19abb93fbdb3b2ec79aa0">32bbc451</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2015-09-22T16:17:26+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix synopsis and vcs-browser
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/477fe9904a0796483bb9d5f0de6f89b3f25d1f1b">477fe990</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2015-09-22T16:22:47+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add lintian-override to document that the language extensions are used internally
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8a507bc2aa4d250e48d901315dd9ab64d794011f">8a507bc2</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2015-09-22T16:23:33+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix spelling
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9f6248cb89494a43e3d3bcfeeb93d56b5bb66ecc">9f6248cb</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2015-09-22T16:24:22+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Mark as team upload since I do not intend to become Uploader for samtools
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/56c94373396c2d649762ed82a687e6d8b7021855">56c94373</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-10-07T14:05:39+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix typo in conditional [minor]
Also minor nearby style: use INT_MAX for position infinity rather
than 1<<29 or 0x7fffmagic; free() handles NULL pointers itself.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e066deb7f40245578f308c616db1ee23d4e83655">e066deb7</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2015-10-07T16:33:37+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Make merge allow input files with no @HD line
Remove check added in 55c852f that required the first SAM header to have an
@HD line when merging. Previous versions worked if no @HD lines were
present; this allows the new header merge code to do so as well.
The new behaviour is that the first @HD line found on either the file
given in the '-h' option, or any of the input files, will be used. If no
@HD line is found the program will complain, but it will continue and
exit successfully (assuming it otherwise worked).
Some code is included to add an @HD if none was present on the inputs, but
it's currently commented out pending discussion.
Fixes #475
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f44f54d27f43dd32fcbd11d63916b1496eb92ec0">f44f54d2</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-10-08T14:21:33+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Miscellaneous tidy-ups [minor]
Update sam_view.c copyright year. Reformat usage. Remove debugging
"Producing XYZ output" (which appeared even for usage displays).
Update usage and samtools.1 synopsis lines to "[options]" now that there
are lots of options beyond the original few.
Write test/test.pl flag filter clearly.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/834bf7e9c9d4bbf7d60160138f728e7968373e3a">834bf7e9</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-10-08T15:47:12+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge bam2fq improvements (PR #263)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6e4bc5240111a1618347c754a8ff89b79af1ec5f">6e4bc524</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-10-12T15:02:35+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge pull request #476 from daviesrob/merge_no_hd
Make merge allow input files with no @HD line</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/87cdc4a962bca3fc6804f56cdb54ea0f1b13e123">87cdc4a9</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-10-20T13:58:19+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Define and use .EX/.EE macros for examples and code blocks
Removes filling and hyphenation from code examples, formats in Courier
in PS output, and paves the way for <pre>-style formatting on conversion
to HTML. Hat tip @kbradnam. The macros are intentionally named similarly
to Ultrix's similar man macros.
Also add '\" preprocessors-needed header line.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/370c7ea2cf073ecea0a30e59b92fed28417bd9fa">370c7ea2</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-11-11T13:15:23+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge develop's --output-fmt-option changes in bam_sort()
Both this branch (fmtout etc) and later changes on the develop branch
handle -O and format setting in their own ways. This handling is currently
duplicated in this merge and will be fixed clearly in a later commit.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7f2bc8ed9ae07e0fd1147d7ce21b606133d8c52a">7f2bc8ed</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-11-18T16:48:23+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update legacy-attempt heuristics and diagnostics
Remove this branch's format setting code, as this is already handled
by the code merged in from the develop branch.
Remove "-o followed by another option" heuristic as the scenario it
handles (legacy "-o -n in.bam tmp") is always already detected by the
"legacy <out.prefix>" test.
Add heuristic to detect legacy "-o in.bam tmp", to the extent that can
be distinguished from modern "-o out.bam in.bam" (namely opening "tmp"
for reading fails and it doesn't have a .bam/etc extension).
Note the historic usage and how to move away from it in the man page.
Add obsolete invocation test cases.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d637d5964ed82d0245a9e8395ef1661a0f1d93a5">d637d596</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-11-18T17:03:57+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Avoid memory leaks on invocation error abends
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a99720588618d78290ca8a783cf0b6f3364c2691">a9972058</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-11-20T10:49:42+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge legacy sort usage removal (PR #441)
[NEWS]
* The obsolete "samtools sort in.bam out.prefix" usage has been removed.
If you are still using -f, -o, or out.prefix, convert to use -T PREFIX
and/or -o FILE instead. (#295, #349, #356, #418, PR#441; see also
discussions in #171, #213)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/40404966f2008a951b63affb5bf88db837cc2769">40404966</a></strong>
<div>
<span> by Shane McCarthy </span> <i> at 2015-11-20T14:00:30+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Document "*" region query for unmapped read pairs
(Use bold instead of extra quoting to avoid confusion for '*', which
needs to be quoted on the command line.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3af0bec60bc2632032ee65a4d6d176dcf73ea113">3af0bec6</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-11-20T14:25:11+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Describe $HTS_PATH, the search path for HTSlib plugins
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f2c357cb854e3c84522840af5416767dae352c60">f2c357cb</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-11-20T15:43:07+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Reformat merge usage
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/fe1868b084cff67a3f5afb036a6b6ba4942dca7a">fe1868b0</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-11-20T16:13:54+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update merge -cp usage
Update merge -cp usage to clarify we use the first line with a given ID
rather than merging the actual lines (fixes #482)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4d56437320ad370eb0b48c204ccec7c73f653393">4d564373</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-11-26T17:24:52+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Improve error messages for opening or format errors
Take advantage of samtools/htslib@6462e349d16e83db8647272e4b98d2a92992071f.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/97c9883e139a127a8b36353b0e7ec12c8319ef38">97c9883e</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2015-12-08T15:09:23+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Rename bamshuf to collate
Now that bamshuf can handle CRAM files we have renamed it so that
it has a more appropriate name.
[NEWS]
* The "bamshuf" command has been renamed to "collate" (hence the term
bamshuf no longer appears in the documentation, though it still works
on the command line for compatibility with existing scripts)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/90dcd90135c7fd134e10b243f646bfb24b600cc0">90dcd901</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-12-09T12:27:29+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Allow for n_targets==0 in finish_merged_header() shrinking
The realloc() function might return NULL when asked to resize to zero
bytes. It is near impossible to correctly distinguish NULL-as-resize-0
(incoming ptr freed) and NULL-as-realloc-failed (incoming ptr not freed):
see WG14 defect report 400 and Austin Group issues 400, 526, and 688.
Avoid all this by simply setting target_name and target_len to NULL when
n_targets==0, leaving merged_hdr->target_name/len to be freed later by
free_merged_header().
Fixes #495. Hat tip to @daviesrob for identifying the cause.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/803143bf2e7004349d1797ca4d17b0b1b355f98b">803143bf</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2015-12-14T12:24:11+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Made --threads long option versions of -@.
(Rebased from PR #472.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/defd753b7abc22ca6f49c513cec92403265602c7">defd753b</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-12-14T13:11:37+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use $(htslib_kfoo_h) make variables for htslib/k* headers
Using these variables allows them to be empty when samtools is compiled
against an installed htslib rather than a development htslib.
See also samtools/htslib@90525e00acb218a6b047eff08473c92f2ef3ec6e.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ea6d10c8dd98bd6b57c8dd96506f321fe50c4755">ea6d10c8</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-12-15T17:44:11+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add configure.ac script
Use autoconf to generate a configure script. Searches for your HTSlib
source tree or installation (fixes #275, fixes #414), checks for curses,
zlib, etc, and emits hopefully informative errors if anything is missing.
Split $(HTSLIB) into $(HTSLIB) (for prerequisites) and $(HTSLIB_LIB) (for
link commands) so that they can be different (empty, -lhts) for building
against an installed HTSlib.
Unconditionally include config.mk from the Makefile, and add rules to
generate basic config.mk/.h (using ../htslib as before) if configure has
not been run. This don't-need-to-use-configure mode will likely disappear
in the near future.
Use AX_WITH_CURSES to detect curses flavour, including determining the
name of the library to link against. Fixes #269, fixes #346, hopefully
improves #66. Add config.h to bam_tview_curses.c; (TODO) eventually it
should be included by all C files, but at the moment config.h contains
only curses-related defines.
AX_WITH_CURSES is from autoconf-archive, and AX_WITH_HTSLIB will soon be
submitted there.
Providing install-sh is a prerequisite for AC_CONFIG_SUBDIRS, which
AX_WITH_HTSLIB uses. (TODO) Use AC_PROG_INSTALL to set $(INSTALL) et al.
(This is the current install-sh from Gnulib.)
(TODO) Update INSTALL and other documentation.
[NEWS]
* Samtools now has a configure script which checks your build environment
and facilitates choosing which HTSlib to build against. See INSTALL
for details
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3c15c88a0b0b64700a67a19446e689f18996b6f5">3c15c88a</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-12-15T17:44:15+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Always link with -rdynamic/-ldl [hack]
As a quick hack to make plain "make" work in both typical HTSlib
scenarios (plain HTSlib; HTSlib configured with --enable-plugins),
add -rdynamic and -ldl to link commands ALWAYS. In future, we would
prefer to communicate the exact linking needs from HTSlib via perhaps
htslib.pc and/or more configure delving.
Introduce $(ALL_LIBS), which will outlast this hack being reverted.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4b4e6880c8c7c4d6cf8ca5b6d3bb4227f7681048">4b4e6880</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-12-15T17:44:28+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update INSTALL etc to discuss configuring samtools
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ed3191b1c4ce76345d16a1020843202bd5d6c6e3">ed3191b1</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-12-15T21:26:20+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Samtools release 1.3: many improvements, bug fixes, and new commands
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/493b1ca6f5ea8c887042fce92ec364b15ab27b4d">493b1ca6</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-12-15T23:14:27+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge version number bump and NEWS file from master
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3c197df845a7f7dae48867a2bc399474cd942936">3c197df8</a></strong>
<div>
<span> by María de Antón </span> <i> at 2015-12-18T17:10:56+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>set a matrix.include for all os options
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0777f64201bd5b2f3ec128a771351f840bebd9aa">0777f642</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2015-12-21T13:24:01+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix Mayhem issues caused by unlimited reads of gz input
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/95188c1fce13f04f507f4ef60c2b6dc8f9355edd">95188c1f</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2015-12-21T13:48:54+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Provide some more manpages
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/663b1a8ea3a586962d3fb99454ea5584411a2a3b">663b1a8e</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2015-12-21T13:49:12+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4a5274b48c80c97f05bb2f78215ad1a5d7c4083c">4a5274b4</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-12-24T13:50:30+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge branch 'debian/unstable' of git+ssh://git.debian.org/git/debian-med/samtools into debian/unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/95c561dc652f4d762d562504f52935270d585ab2">95c561dc</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-12-24T13:55:19+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge tag '1.3' into debian/unstable
Samtools release 1.3: many improvements, fixes, new commands
* The obsolete "samtools sort in.bam out.prefix" usage has been removed.
If you are still using -f, -o, or out.prefix, convert to use -T PREFIX
and/or -o FILE instead. (#295, #349, #356, #418, PR #441; see also
discussions in #171, #213.)
* The "bamshuf" command has been renamed to "collate" (hence the term
bamshuf no longer appears in the documentation, though it still works
on the command line for compatibility with existing scripts).
* The mpileup command now outputs the unseen allele in VCF/BCF as <*>
rather than X or <X> as previously, and now has AD, ADF, ADR, INFO/AD,
INFO/ADF, INFO/ADR --output-tags annotations that largely supersede
the existing DV, DP4, DPR annotations.
* The mpileup command now applies BAQ calculations at all base positions,
regardless of which -l or -r options are used (previously with -l it was
not applied to the first few tens of bases of each chromosome, leading
to different mpileup results with -l vs. -r; #79, #125, #286, #407).
* Samtools now has a configure script which checks your build environment
and facilitates choosing which HTSlib to build against. See INSTALL
for details.
* Samtools's Makefile now fully supports the standard convention of
allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden as needed.
Previously it listened to $(LDLIBS) instead; if you were overriding
that, you should now override LIBS rather than LDLIBS.
* A new addreplacerg command that adds or alters @RG headers and RG:Z
record tags has been added.
* The rmdup command no longer immediately aborts (previously it always
aborted with "bam_get_library() not yet implemented"), but remains
not recommended for most use (#159, #252, #291, #393).
* Merging files with millions of headers now completes in a reasonable
amount of time (#337, #373, #419, #453; thanks to Nathan Weeks,
Chris Smowton, Martin Pollard, Rob Davies).
* Samtools index's optional index output path argument works again (#199).
* Fixed calmd, targetcut, and potential mpileup segfaults when given broken
alignments with POS far beyond the end of their reference sequences.
* If you have source code using bam_md.c's bam_fillmd1_core(), bam_cap_mapQ(),
or bam_prob_realn_core() functions, note that these now take an additional
ref_len parameter. (The versions named without "_core" are unchanged.)
* The tview command's colour scheme has been altered to be more suitable
for users with colour blindness (#457).
* Samtools depad command now handles CIGAR N operators and accepts
CRAM files (#201, #404).
* Samtools stats now outputs separate "N" and "other" columns in the
ACGT content per cycle section (#376).
* Added -a option to samtools depth to show all locations, including
zero depth sites (#374).
* New samtools dict command, which creates a sequence dictionary
(as used by Picard) from a FASTA reference file.
* Samtools stats --target-regions option works again.
* Added legacy API sam.h functions sam_index_load() and samfetch() providing
bam_fetch()-style iteration over either BAM or CRAM files. (In general
we recommend recoding against the htslib API directly, but this addition
may help existing libbam-using programs to be CRAM-enabled easily.)
* Fixed legacy API's samopen() to write headers only with "wh" when writing
SAM files. Plain "w" suppresses headers for SAM file output, but this
was broken in 1.2.
* "samtools fixmate - -" works in pipelines again; with 1.0 to 1.2,
this failed with "[bam_mating] cannot determine output format".
* Restored previous "samtools calmd -u" behaviour of writing compression
level 0 BAM files. Samtools 1.0 to 1.2 incorrectly wrote raw non-BGZF
BAM files, which cannot be read by most other tools. (Samtools commands
other than calmd were unaffected by this bug.)
* Restored bam_nt16_nt4_table[] to legacy API header bam.h.
* Fixed bugs #269, #305, #320, #328, #346, #353, #365, #392, #410, #445,
#462, #475, and #495.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/824f68f0227076c1e4573d894f3ee89a54632618">824f68f0</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-12-24T13:59:30+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream release; no new copyright nor license notice.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/86a93751b87ad21154b8068d06e15d84f080edeb">86a93751</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-12-24T14:02:04+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Replace LDLIBS by LIBS, following upstream changelog.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c12f4f35b82b40a6b3d44236a89c543bac210bd9">c12f4f35</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-12-24T14:08:27+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Removed patch; issue solved upstream.
https://github.com/samtools/samtools/pull/286
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5c4ca0b5309fa25e1ecd6790ad6eec269a75789f">5c4ca0b5</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2015-12-24T14:09:58+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Removed patch; issue solved upstream.
https://github.com/samtools/samtools/issues/305
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/befba2ea217f61f1c579b657fa0e1b315cbfa090">befba2ea</a></strong>
<div>
<span> by John Marshall </span> <i> at 2015-12-31T13:07:37+13:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Include <unistd.h> for isatty() [minor]
We get <unistd.h> as a byproduct of zlib.h and getopt.h on Linux and OS X,
but not on FreeBSD.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/de68be6ca3964aebd5b49e024824d6a7c0cfd617">de68be6c</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-01-03T09:19:41+13:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Happy New Year
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/664cc5fee8d8f75add2d6bf79db3f74465a7b723">664cc5fe</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-01-05T00:01:26+13:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed a known-failure (mpileup -d) issue; now passes.
samtools/htslib@df4a80e9c387bb1d84cdb47c02e44e77b0f57770 has removed a
dummy field from the pileup structure. In doing so this decrements the
number of items in the mp pool by 1, which coincidentally was the cause
of the maximum depth field being out by one. Bonus!
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/74a3e0a744f91bc2b1f65a4144a509d6dd791631">74a3e0a7</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-01-28T10:56:56+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add #include <config.h> to all *.c source files [minor]
Upcoming config.h settings will have ODR implications, so ensure all
source code sees these settings.
Also add missing faidx.o rule.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4988ce7af84ee295f63c93f3185aeea407071ade">4988ce7a</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-01-30T21:23:51+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>adapt to new build system
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/45397bc4edcd2da0e80e18fc3e75c54800302847">45397bc4</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-01-30T21:23:51+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>use secure Vcs-Git
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f1e3f7c8ee30f890f8bd8fbb07278b8e99a93666">f1e3f7c8</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-01-30T21:23:52+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>patch configure.in to not call make in m4_esyscmd_s()
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6479cce74c8a54356d3cb72293378cb465799b36">6479cce7</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-01-30T21:23:52+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>add Build-Dep to automake
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/487e759e70a8dfc77c7d23b1aa085d2a6f9d75ef">487e759e</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-01-30T21:23:53+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>cleanup copyright
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d985799b2098bde92d27bae258612856b3c41a41">d985799b</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-01-30T21:31:14+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>add patch header
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/82f34d3480d43b8fe8d895c23ccffeeebc865e52">82f34d34</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-01-30T21:38:54+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>patch spelling
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/59ab663fb9c98bd454432070fd09bc13b7c488bc">59ab663f</a></strong>
<div>
<span> by Martin Pollard </span> <i> at 2016-02-02T13:34:15+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix -O option for reads without OQ tag
When using the -O option the +1 meant our NULL check was failing. Fix to only
populate oq variable where there is an OQ tag present. Fixes #517
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/03a6bc5b2de2f4cde266ee914f8b6ba3753001f3">03a6bc5b</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-02-02T14:12:21+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Improved documentation of mpileup -l vs -r.
Fixes #128 and #130.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9d12a17a18b199d4cf9245195112906e323d877b">9d12a17a</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-02-03T10:13:39+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>update d/changelog
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a9bf06a38a1061418cd19b0f63e855b43b661c36">a9bf06a3</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-02-05T08:29:26+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>add NEWS for 1.3 commandline API changes
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/096bc41752fe26844633cde88a7614cfde51c280">096bc417</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-02-05T08:32:52+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>dch -r
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/23b91e87e22ddc0555b24f365ada60d8c361f300">23b91e87</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-02-05T17:26:12+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Improved documentation of how mpileup -d/-L work.
They're still quirky, but at least it's documented quirks!
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a5cdff681b582f135eebcd2177890085cb2a3a7a">a5cdff68</a></strong>
<div>
<span> by Ben Taylor </span> <i> at 2016-02-08T14:45:45+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove gcc build on OSX
It's just using clang anyway:
https://travis-ci.org/samtools/samtools/jobs/107289030#L37</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c6131472f979d831734d3961e95e3fe2d8773109">c6131472</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-02-09T15:13:24+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Tidied up the mpileup.[123].sam files to not use RNAME fields with no @SQ records.
I could have added the entries to the @SQ records, but this may have
caused more problems given we don't have the full chr17, just 4200
bytes of it and the mini-sequence in the ref.fa file. Side-stepping
the whole CRAM and reference-required issue is the route of least
resistance.
Fixes #489
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c152c47ba016d5f18c15ede7e99cbf4cfe639264">c152c47b</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-02-11T11:20:17+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix typo.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3d792baf65fe61979525bc21d3dee46b6584814e">3d792baf</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-02-11T11:21:07+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge pull request #525 from samtools/mpileup_depth
Improved documentation of how mpileup -d/-L work.</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/bf8544023cccfd4c090b3daab5633f1b5da1b4e7">bf854402</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-02-11T12:04:17+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Grammar fix.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/dae373be3c93f10bde29098fd984adde5e399ce0">dae373be</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-02-11T14:27:54+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Ignore .exe extension; don't force core and ~ ignorance
Some developers prefer not to have core and *~ be ignored, and
settings here in .gitignore cannot be overridden. Those who do
want them ignored should add local entries in $GIT_DIR/info/exclude
or in their core.excludesfile.
(Remove /bgzip entry, which has long since moved to htslib.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ac5b8e7c96836d2ef898d9623173fcad54f4cdce">ac5b8e7c</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-02-11T15:54:04+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use AC_SYS_LARGEFILE configure test instead of -D_FILE_OFFSET_BITS=64
Defines _FILE_OFFSET_BITS etc in config.h as appropriate. On 64-bit
machines we don't need it, and it was just noise in make log output.
On 32-bit machines it now exactly parallels the settings applied in
HTSlib post samtools/htslib@f1327a703583bf61e2e7ffd11198487fee2a8422.
On 32-bit machines it is now *required* to run configure in order for
large files to be usable. But it'll likely soon be non-optional for
everyone anyway.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ce44eb37f5cdc88fefd07d972d7b6848a8ec3ad6">ce44eb37</a></strong>
<div>
<span> by Martin Pollard </span> <i> at 2016-02-16T15:28:26+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add check on hts_close to quickcheck
Add check on hts_close to quickcheck command, we are missing some errors here.
Add expected_fail test for CRAM file missing EOF block.
[JM: Add to quickcheck/all test, with expected_fail.]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6e3ac2707d2b6ea80d5e02d31366d0efc4fb1ee1">6e3ac270</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-02-17T12:18:03+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed bam_get_library() crash.
This was triggerable from samtools rmdup or samtools view -l when an
@RG header was present without an LB: record.
I also fixed the samtools view -l logic. The man page states that it
only shows reads in that library, while the implementation was to only
show reads in that library or those where it could not determine the
library.
Fixes #538
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2dcdd6206550aff3c52a4fec2b3e97b826f21698">2dcdd620</a></strong>
<div>
<span> by Joshua C. Randall </span> <i> at 2016-02-22T15:51:06+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Adds a usage note to `samtools quickcheck`
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d49c73b9ce5f0b169f82d8c79e2e411a581dc5c7">d49c73b9</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-02-22T16:16:28+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Reformat "Notes" in long -? usage output
Make code examples stand out more. Drop excess `foo' and `bar` quoting.
Use 'fail!' rather than "fail!" as the latter invokes the history mechanism
in Bash.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3c8a69f0055c4e5940962294d7e788e016bea715">3c8a69f0</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-02-23T14:35:22+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix samtools merge -n usage doc [minor]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/de96bfb6100645541cec1b5c1119a9a16f5820ec">de96bfb6</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2016-03-08T14:22:46+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix warnings from adding HTS_RESULT_USED to htslib prototypes.
Companion to PR samtools/htslib#271. Add checks to return values from
functions now marked with HTS_RESULT_USED in htslib. Also fix some other
obvious places where errors were not handled correctly. Try to improve
cleanup code so that memory is not leaked and files are closed, even when
exiting due to an error.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0e260d917477da4c2323530ac973fd0245a2eded">0e260d91</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2016-03-08T14:35:23+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Ensure fp is always closed in write_buffer.
Prevents file descriptor leak on errors. Hat tip to
godotgildor's pull request https://github.com/samtools/samtools/pull/253
which is duplicated in this patch. I would have merged it in if I'd
noticed it earlier...
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f63a28226a63742c84e4647f5b7d02df69a1f444">f63a2822</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-01T15:01:42+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Recreate missing @SQ header from BAM binary header
Some tools create BAM files with no text @SQ headers, which is unusual
but nonetheless valid. Create a basic dummy header from the binary
header, as we may be merging with another file that does have @SQ
headers and having some but not all is not valid.
Fixes #548 and fixes #550.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/cd7e0051d443415342d4bc71c94c7a9a403ba994">cd7e0051</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-03T10:16:57+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix indentation [minor]
Hat tip @zfrenchee.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3baa47bc4bb5de43119defeedc640a317a3c8d5a">3baa47bc</a></strong>
<div>
<span> by Shane McCarthy </span> <i> at 2016-04-06T09:04:07+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>manpage: fix typo [minor]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/09dda53c46f6b205595101082adff43a972f1982">09dda53c</a></strong>
<div>
<span> by Shane McCarthy </span> <i> at 2016-04-06T09:06:19+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>fastx: only show relevant usage options for fasta/fastq commands
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3312225626e842092e73313801c3e3e709f4026f">33122256</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-06T11:34:12+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge fasta usage message improvements (PR #555)
(Hopefully simpler with multiple printfs.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6994f30af178de66c7ad3900186b714cbd589b06">6994f30a</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2016-04-07T10:37:21+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Check sam_read1() return value correctly
BAM returns different values to SAM and there was a silly mistake in
the code that checked that value. (Fixes #532)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/54a91c14965d8ba9bd82fdb99351567bcf0b5d5b">54a91c14</a></strong>
<div>
<span> by George Hall </span> <i> at 2016-04-12T15:14:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Implemented tab completion
I have added a script which determines all Samtools subcommands and the
options available for these subcommands. It then generates a file which,
when sourced in Bash, allows for tab completion of all subcommands, and,
when appropriate, the long options for the relevant subcommand.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/24d3235d5ce920592a9f17ee947d5b72749b0eb6">24d3235d</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-13T10:23:07+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use print_error_errno() where appropriate
Use it in error-checking code new to this branch and when reporting
errors from opening files (cf #51). Not used in bam_sort.c and
bam_split.c as these are also compiled into test/merge/* and
test/split/* test programs, which cannot be linked with bamtk.c.
(TODO) Move print_error()/etc to sam_opts.c, and merge samtools.h/
sam_opts.h/sam_opts.c into sam_utils.[ch] or similar.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/fd02fc5614bd7ef6214c4bddcf4d941000670f95">fd02fc56</a></strong>
<div>
<span> by George Hall </span> <i> at 2016-04-13T12:36:56+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Dynamically generate options
As was apparently mentioned at the meeting, it is probably better to
dynamically generate tab completions rather than to generate a one-off
script which the user then stores. This is what this new version does -
possible completions for subcommands and long-options are generated
on the fly, meaning that it is no longer necessary to try and keep the
completion file up-to-date. Additionally, this allows for support of
mulitple versions etc, by append lines to the bottom of the file, as
noted in the comments.
I have removed the previous version.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/248534509594ea30f95eec30cf7f30129d332a6a">24853450</a></strong>
<div>
<span> by George Hall </span> <i> at 2016-04-13T14:21:25+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Cleaned up subcommand name retrieval
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/193eecb56d255aaa703644a9d4d39fbdd73b3f7e">193eecb5</a></strong>
<div>
<span> by George Hall </span> <i> at 2016-04-13T14:28:58+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Changed '==' to '-eq'
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/115288181e70e7742dbb17d9ad66b23bf0d746a7">11528818</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-14T14:27:56+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Various tidying up and segfault fixes
bam_cat.c: fix exit status.
bam_rmdup.c: clean up even when bam_rmdup_core/bam_rmdupse_core fails.
bam_rmdupse.c: use the usual -1=>error convention.
bam_sort.c: fix new "samtools merge -f out.bam nonexistent.bam" segfault.
bamshuf.c: reuse bam1_t structs in `a`, simplifying destroying them
in case of error.
padding.c: fix existing "samtools depad nonexistent.bam" segfault,
fix exit status.
phase.c: rewrite file open loop as function, fix exit status,
(TODO) note memory/file descriptor leaks still present.
sam.c: don't bam_hdr_destroy() the user's aux; when sam_hdr_write()
fails, return NULL irrespective of bam_verbose.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f6db7827764c375f8ca30d026cc4e8e2b2fdab7a">f6db7827</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-14T14:44:04+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge error checking improvements (PR #467)
Companion to PR samtools/htslib#271. Add checks to return values from
functions now marked with HTS_RESULT_USED in htslib. Also fix some other
obvious places where errors were not handled correctly. Try to improve
cleanup code so that memory is not leaked and files are closed, even when
exiting due to an error.
Note that this introduces duplication of cleanup code (there's the
normal flow, and there's goto-fail cleanup that needs to deal with
partially-initialised data structures) in several source files.
(TODO) Large amounts of duplicated cleanup code in bam_rmdup.c,
bam_rmdupse.c, bam_sort.c, and bamshuf.c that could perhaps be
refactored to duplicate less code.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/72679e1f6e3d9924f3be9bae4e2f61cd4e5264d9">72679e1f</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-14T14:55:28+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix \r\n thinko [minor]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0bfa8d4249fc4035043e1aa3bb63bca0cdf6f7e3">0bfa8d42</a></strong>
<div>
<span> by George Hall </span> <i> at 2016-04-14T16:55:32+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Captialised variables for consistency
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2389a31d83b6baf8dd8cfc6005a32ab5e5798d6a">2389a31d</a></strong>
<div>
<span> by George Hall </span> <i> at 2016-04-15T12:51:09+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed slight bug in default behaviour
Now handles files with spaces in their names correctly.
In doing so, I have basically made the change mentioned here:
https://github.com/samtools/samtools/pull/560#discussion-diff-59540631 I
have made the change in a slightly different location, however, as this
has the advantage of not allowing the user to expand '/' or similar when
they should be entering a subcommand (i.e. when completing the first
argument).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9968e4c38fa3f066b9e18d39f8a1bc724aa4052e">9968e4c3</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-04-18T10:47:12+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Make samtools sort notice when it clobbers other sorts
The temporary filenames still aren't unique; the same filenames
generated when opening and then again when unlinking, so fixing this
properly requires larger code reorganisation.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5f53e3cd184a47b51f921a18402fc8bad8a39877">5f53e3cd</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-19T13:31:56+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Propagate errno from sort worker threads
Return errno to the main thread, and on failure print it in an error
message. Improve other I/O-related error messages to show errno (cf #51).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b5047ab4b6f4d3d199e4e95bc91b960b29acc7a1">b5047ab4</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-04-21T12:10:01+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Removed a (harmless) perl warning from test harness.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8471a0d77be2a39276992b59d139ce7a4c8d3951">8471a0d7</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-21T14:18:58+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add `@CO` headers only once when merging sort temp files
Add MERGE_FIRST_CO for samtools sort (but don't expose it via the
merge command). When set, bam_merge_core2() will copy `@CO` headers
from only the first file to be merged, so when a large sort produces
several temporary files to be merged, the headers won't be duplicated
in the final output.
This is a quick semi-hack to fix #563; there may be better ways to
fix this with greater refactoring. See #390 for discussion of why
this simplistic approach is not suitable for samtools merge in general.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5839af65d2d834aa759eced0ba07fbcc2b109b70">5839af65</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-22T09:19:42+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Write sort's temporary files alongside the *output* file
If several sorts are running simultaneously, the output filenames are
more likely to be distinct than the input filenames (which might often
be standard input). This is a return to the pre-PR #441 behaviour.
If -T specifies a directory or the output is standard output, add a
random component to the prefix to try to avoid collisions. (For output
to stdout with -T not specified, collisions would otherwise be certain.)
Fixes #523, fixes #535, et al.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/897c0027a04501e3ea33d94b5cdeb633d010da8d">897c0027</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-22T10:22:44+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Samtools release 1.3.1: bug fixes, notably sort temporary file fixes
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7d3f3a8fc23dd5e640bbc2d978cb6e3182806c78">7d3f3a8f</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-22T14:48:37+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge version number bump and NEWS file from master
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9627ffb918f91cbbcaef71b1ede817f1ff990207">9627ffb9</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-25T13:47:35+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>HTSlib now provides errmod_cal() etc
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a60dd3786af8c5c94a84df44e0ea622697c4ad61">a60dd378</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-26T09:48:31+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use HTSlib's new sam_prob_realn() and sam_cap_mapq() functions
Samtools's bam_prob_realn_core() and bam_cap_mapQ() have been moved
to HTSlib (with slightly altered names).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0c961b23afec6697b7dbe7cc91e246f694b9ac1e">0c961b23</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2016-04-26T20:39:39+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge tag '1.3.1' into debian/unstable
Samtools release 1.3.1: bug fixes, notably sort temporary files
* The sort command creates any needed temporary files alongside the final
output file (similarly to the pre-1.3 behaviour), and now aborts when
it detects a collision with another sort invocation's temporary files.
When the -T PREFIX option specified is a directory (or when sorting to
standard output), a random component is now added to temporary filenames
to try to avoid collisions (#432, #523, #529, #535, PR #530).
* All samtools commands now check for I/O errors more carefully, especially
when writing output files (#111, #253, #470, PR #467).
* Build fixes for 32-bit systems; be sure to run configure on such systems
to enable large file support and access to 2GiB+ files.
* The fasta/fastq/bam2fq command no longer ignores reads when the -s option
is used (#532).
* The fastq -O option no longer crashes on reads that do not have an OQ tag
field (#517).
* The merge and sort commands now handle (unusual) BAM files that have no
textual @SQ headers (#548, #550).
* Sorting files containing @CO headers no longer duplicates the comment
headers, which previously happened on large sorts for which temporary
files were needed (#563).
* The rmdup and view -l commands no longer crash on @RG headers that do not
have a LB field (#538).
* Fixed miscellaneous issues #128, #130, #131, #489, and #514.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0de58f79d6c25a3fd7869bd0870163a2e424b088">0de58f79</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2016-04-26T20:42:02+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream release; no new copyright nor license notice.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3666b08edb66c6bd1597552348b883370e8a2cb2">3666b08e</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2016-04-26T20:57:11+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Conforms with Policy version 3.9.8.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/82c3bfa5864096b40617beaca72d125fff7710a7">82c3bfa5</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2016-04-26T20:58:18+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove legacy statement on the libbam.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/60c45b7e8943124488c9cdbc231e32d8c95316c8">60c45b7e</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2016-04-26T21:12:25+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>samtools (1.3.1-1) unstable; urgency=medium
0c961b2 Merge tag '1.3.1' into debian/unstable
3666b08 Conforms with Policy version 3.9.8.
-- Charles Plessy <plessy@debian.org> Tue, 26 Apr 2016 21:12:05 +0900
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f846d657399a7ea22d00198a53796249c56931d3">f846d657</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-26T13:27:54+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use HTSlib's new probaln_glocal() function
Samtools's kpa_glocal() has been moved to HTSlib (with a slightly
altered name).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4f9a327468ed33e71ec0d1d3775886ba35175b93">4f9a3274</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-04-26T15:29:00+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use HTSlib's new errmod_cal()/probaln_glocal()/sam_prob_realn() functions
Requires samtools/htslib@b183ab2d5abbff4592074b3ba177d84e550a7e3b (PR samtools/htslib#343).
Our errmod.[ch] conflicts with that added to HTSlib, so must be removed to
work with samtools/htslib@55b2ae462619538b27cf64f518b03f4b56bb421a or later.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/952da102acfa75de77f1b5902b10aa3f065f181d">952da102</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2016-04-27T10:02:02+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Needs htslib 1.3.1.
Closes: #822701
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0296398891f288d2f2be78654d3b699f2bceb8f4">02963988</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2016-04-27T10:03:06+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Current changelog.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9e4093d242eb671ae0d25315793cfbf4aad04f9c">9e4093d2</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-05-06T15:09:48+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Explicitly set @CURSES_LIB@ for --without-curses
If for some reason AX_WITH_CURSES is not expanded, autoconf will
never see CURSES_LIB/etc marked as output variables and not expand
@CURSES_LIB@/etc. As AX_WITH_CURSES is within a conditional, this is
particularly confusing for --without-curses. Fixes #528, but alters
nothing in normal circumstances.
(Set CURSES_LIB/etc to empty separately rather than with
AC_SUBST([CURSES_LIB], []), as with the latter the new code is
expanded to "else fi", which is a shell syntax error.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a98b89bbd5e258c91e86100ad275aa1d031590f8">a98b89bb</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2016-05-08T21:11:34+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>samtools (1.3.1-2) unstable; urgency=medium
952da10 Build-depends on htslib 1.3.1. (Closes: #822701)
-- Charles Plessy <plessy@debian.org> Sun, 08 May 2016 21:11:12 +0900
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/026c8d7fbd42e3364a7a54f51cb7c1a10b222d1e">026c8d7f</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-05-10T14:11:47+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Write BQ SAM line the same way as for AF
Avoid puts(NULL) and only clear kstring_t if write_cns is true.
Detected via GCC 6 -Wmisleading-indentation warning.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e4446b5aeebba4b1225843cc542bf7cce07e48c9">e4446b5a</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-05-11T11:03:41+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use bcf_hdr_format() rather than deprecated bcf_hdr_fmt_text()
Uses new HTSlib function added in samtools/htslib@f581de8b6714cf69416ce6f9d4d4f050996699b8.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e5dfb0aa444c9dc0e4e80219690167af757b68ef">e5dfb0aa</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2016-05-13T15:03:01+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add samtools view tests for extracting unmapped reads.
Add test to make samtools view search for region '*', i.e. unmapped reads.
Add an extra reference (ref3_unused) to view.001.sam, view.001.fa and
view.001.fa.fai. This reference is the last in the header, but is not
used in the body of the file.
Detects the (htslib) bug described in issue samtools#568 (samtools
index/view bug with unmapped reads).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1c1c219679b74f10606f8c23e447e253cbdf30a6">1c1c2196</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-05-17T14:44:56+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed the out by one error in --insert-size.
Fixes #345.
(Changes proof-read by @daviesrob)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b4e452c3a0703d401b0e388b9b646e7495f13456">b4e452c3</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-05-17T16:57:09+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added mpileup -a and -aa options
Fixes #496. Also fixed the tests for c1#pad1.bam and c1#pad2.bam;
they should have been known failures instead of know passes (see
issues samtools/htslib#57 and samtools/htslib#59).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/69567c8ab602df9a41e75405646eed0adab86f59">69567c8a</a></strong>
<div>
<span> by Martin Pollard </span> <i> at 2016-05-18T10:41:25+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>bam2fq_mainloop should be using filter_it_out
Remove duplicated code bam2fq_mainloop should be using filter_it_out rather than it's own copy of those lines.</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/402aa76d9cf15a06277af0e44e7282e616857401">402aa76d</a></strong>
<div>
<span> by Matthieu Foll </span> <i> at 2016-05-18T16:54:40+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed the `-a` option for zero coverage positions
Fixes https://github.com/samtools/samtools/issues/374 after my [comment](https://github.com/samtools/samtools/issues/374#issuecomment-219427442)</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4dbadcfd3f0c439c21def9ed24a125afa2a3d66f">4dbadcfd</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2016-05-19T12:27:28+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Enforce a minimum memory requirement for samtools sort
Prevent accidents where sort creates one temporary file per input read
by refusing to run unless the -m parameter is set to at least 1 MiB.
If it doesn't run, it prints an error message explaining in detail why
not.
Includes a note in the man page describing the limit.
[NEWS]
* To stop it from creating too many temporary files, samtools sort will
now not run unless its per-thread memory limit (-m) is set to at least
1 Megabyte.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4db01dd8c741ed4bce9030fd6f2561432e629d51">4db01dd8</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-05-19T16:53:04+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Improved error reporting in samtools index.
Along with the same named htslib branch, this fixes samtools#312.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b2b81b4d0cda69c823f4b0fba608386021241542">b2b81b4d</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-05-20T15:10:34+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge sort memory requirement diagnostic (PR #581)
(Unindented the string text to improve 80-column legibility of the
source code.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4f8adc8fea3d80a613e1f0865cf662b77ad1757a">4f8adc8f</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-05-20T15:15:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add NEWS item about mpileup zero coverage '*' fixes
Mention the output changes due to b4e452c3a0703d401b0e388b9b646e7495f13456
(see PR #537); they're surely minor, but it turns out they've been noticed:
https://sourceforge.net/p/samtools/mailman/message/35102141/ (samtools-help,
"Question relating to samtools mpileup output", 2016-05-19).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d0c09f35bf7e3373db3c8849ba466cbeb4a2de3d">d0c09f35</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2016-05-23T14:01:35+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Convert quickcheck to hts_check_EOF API to check EOF on CRAM
Convert quickcheck to hts_check_EOF API to check EOF on CRAM files and
avoid using BGZF internal APIs.
Add tests for samtools generated cram 3.0 and 2.1 (previous truncated
file was generated using scramble).
Make EOF check work on non-sequence data.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/44290ddc3c8808cd82689d6f206c47fb112a59a1">44290ddc</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-05-25T14:21:17+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Depth/Mpileup -a fixes. Fixes #374.
These work with and without regions (-r). With bed files it's more
challenging. They mostly work, but the distinction between -a and -aa
is blurred and bed regions that are entirely absent of data may be
omitted even with the -aa option.
It is possible to fix this, but it will need surgery on the bed
parsing code which these changes don't touch. (Bed processing is
currently a completely opaque data structure with a minimal API.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9c5fd9813b3cd2bea176a59dbc67507969a1c7fd">9c5fd981</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-05-25T14:22:47+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added 30ish new tests for depth/mpileup -a and -aa.
Fixes samtools#374
Note that there is one case for each that is listed as a known
failure. If we use -a with a BED file and the BED file specifies a
region which has zero coverage, but that reference has coverage
elsewhere (and we are not using -r to filter out that region), then
the output will still include zero data for the BED region.
Thus in this scenario -a is acting as -aa should. Fixing this is
tricky, but probably there is little desire to use BED with the
inbetween -a (rather than -aa or no 'all' option).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1395f125eb7baf7d42ea2731b5b69912f7b57342">1395f125</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-05-25T15:59:33+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix Rob and Martin's whitespace [minor]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/675bff76925dd671de3530380bed7a45c91cb4b1">675bff76</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-05-25T16:06:58+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge mpileup/depth -a/-aa fixes (PR #579, PR #586)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2fa144fa85073ad26d23809b9644f2ace1271c04">2fa144fa</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2016-05-25T17:19:10+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Further depth/mpileup tests. Also improved documentation.
Sorry I somehow lost these in a stash while juggling something else
and didn't spot they got missed off the PR. (Already Travis checked on
my fork, but subsequently pushed directly as PR has been merged
already with modified history.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f458b7cc9d2b63cd5b3c68730d2b6777da6b4776">f458b7cc</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-05-26T11:29:57+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Testclean and ignore test temporary files
Now ignores/cleans xx#depth*.bam*, so beware trying to add such files.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/39c4b673870609bce377b290245d6994621fdbe2">39c4b673</a></strong>
<div>
<span> by David K Jackson </span> <i> at 2016-06-01T15:44:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Amend info regarding bedcov subcommand
Correct help message from command to note the -Q INT optional filter
works on mapping quality (not base quality). Report help messages
from depth and bedcov more consistently. Add -Q option to bedcov
entry in man page.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/cbea0f9e4fa5158cb320bd2f18bdf97720e9050e">cbea0f9e</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-06-02T10:37:12+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Allow finer control over program vs. script installation
Use $(INSTALL_SCRIPT) to install scripts and $(INSTALL_MAN) to install
man pages. Install misc/* programs and scripts to $(misc_bindir),
which is $(bindir) by default but may be overridden.
TODO perhaps add a --with-misc-bindir configure option.
Now that $(MISC_SCRIPTS) is so named, remove BUILT_ from other variable
names so they parallel $(PROGRAMS).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/73c4054a91d6ea357802e85b8a68b2a5c97ce061">73c4054a</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-06-02T11:45:03+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add libst.a so test suite can use print_error()/etc
Move print_error()/print_error_errno() to a new sam_utils.c so
that test programs can use them without getting samtools's main().
Build a new libst.a (but DON'T add it to "lib" or "install" targets,
as it's for internal use here in samtools only) linked against by
both samtools and the test programs, as this sort of shared code
is likely to increase.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/29cfd70110ee809890b2cdbddf6ed99f25553a91">29cfd701</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-06-02T16:22:01+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use print_error/_errno() in bam_sort.c and bam_split.c
Followup to 24d3235d5ce920592a9f17ee947d5b72749b0eb6 now that these
are available to test programs.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a04a7dda28e6ab209d5379c307c202b83ab67197">a04a7dda</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-06-02T16:39:43+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Avoid printing "error message: Success" [minor]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/324d66211ee564d7c360edfd8a812949aed1c658">324d6621</a></strong>
<div>
<span> by jenniferliddle </span> <i> at 2016-06-13T11:33:35+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>bam_split now adds @PG header to bam files (PR #557)
[Use a fixed string version of samtools_version() in test/test.c so
that tests can embed the constant in expected output; similiarly with
test_filter_header_rg.c's stringify_argv() usage. Fix memory leaks.
Update makefile dependencies. -- JM]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f3178b7462c4890e586266615b96d75e4805f83e">f3178b74</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-06-13T17:14:25+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Avoid strndup() and strsep() for portability reasons
strndup() is in POSIX but unavailable on e.g. OS X < 10.7;
strsep() is not a POSIX function.
No need to duplicate the input in confirm_rg() or get_first_rgid() as they
don't modify it, and the header has come from bam_hdr_dup() so hdr->text
is always NUL-terminated.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/91283dd2093f7ce7a2e1bda34db72f12df2aa7ae">91283dd2</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-06-21T15:58:16+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>In read_file_list(), check for URL syntax or extant files
Since 4b0058f506960786fc4c988c512cd462e02f24ed, read_file_list() checks
that the list file actually contains a plausible list of filenames (rather
than e.g. being itself a BAM file). We can't really check that remote URLs
actually exist, so check for valid URI scheme text or an extant local file.
Fixes #592.
TODO Potentially rewrite to use hts_readlist() instead.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b25695bc25268aebe3372696c79fb38a634c2b1a">b25695bc</a></strong>
<div>
<span> by Anton Kratz </span> <i> at 2016-06-21T16:46:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add plot-bamstats -l / --log-y option
Added command line parameter parsing and Gnuplot code to plot the Y axis
of the Insert Size plot optionally in log10 scale.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/26e1ea5b4a58e7bff0fac45c821e7fd2df45261d">26e1ea5b</a></strong>
<div>
<span> by David K Jackson </span> <i> at 2016-06-27T13:52:20+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Clarify bedcov subcommand usage
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/de10fa3e8f3abe74790a263e2d3e8cb2455b879f">de10fa3e</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2016-07-18T13:36:45+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Make samtools faidx write faster and detect write errors.
Replace the putchar() loop in faidx with a call to fwrite. With glibc
the reduction in function call overhead gives a roughly 70% speed increase.
Add checks for write failure, so faidx is more likely to notice if
something goes wrong. Also try to avoid a possible overflow if seq_len
is greater than INT_MAX - 60.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/613501f519f12100286714f59a04889bc3f5db83">613501f5</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-07-18T15:18:52+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Exterminate error(), fix memory leaks in event of write errors
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d1039b9576b4e6a0feb72e45c6e0dd36f149092f">d1039b95</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-08-03T11:03:18+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix language misidentification of test data [minor]
Linguist was identifying test/dat/mpileup.*.[1-9] as groff (man page)
source due to their extensions, inflating the language statistics
shown on the GitHub repository.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9df632114a537f57928e4b2c17fbb1928679f877">9df63211</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-08-22T16:04:33+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use print_error_errno() to report file open failures
Further followup to 24d3235d5ce920592a9f17ee947d5b72749b0eb6;
report errno when reporting errors from hts_open() et al (cf #51).
In cut_target.c, print an error message instead of segfaulting.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a9054c758de25563f4a96c2cb8aa2f5152618233">a9054c75</a></strong>
<div>
<span> by Petr Danecek </span> <i> at 2016-10-07T10:12:09+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Place percent mapped bases output in the correct field
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/04ce2bcc0d4a2198178f63d4c78ae91e27daa119">04ce2bcc</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-10-10T12:45:15+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Improve view -s documentation
If you subsample repeatedly with the same seed value, you end up
subsampling to min(fractions) rather than to product(fractions) as you
would hope if the sampling was independent.
The use of srand()/rand() is really a red herring: we're not seeding the
random number generator to get a sequence of random numbers; rather we're
just using srand()/rand() once to ensure subsam_seed has several bits set
even when the user provides humane settings like 0, 1, 2, etc.
Overloading the -s value to set the seed remains obtuse; cf #217.
Documentation resolves #617 and similar mistakes.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9aac9cbec983831351611d227702fc04b7235948">9aac9cbe</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-10-20T20:03:25+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>fix FTBFS
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ce4a601a0859bc9ccfcf000dddf0ac77e7d576b3">ce4a601a</a></strong>
<div>
<span> by John Marshall </span> <i> at 2016-10-21T13:57:05+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Skip usage tests when pseudo-terminal can't be opened
Put `new IO::Pty` inside the eval too, so that we just skip these
tests in the unlikely event this fails, rather than aborting.
(Further to #300; cf @satta's part of https://bugs.debian.org/840974)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/db8bac6a829060fb990e30fd8b19c28d40500939">db8bac6a</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-10-23T13:35:15+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>use John Marshall's patch to address test pty issue
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/90a26350479e956eb45e6ff98c4e5d034f16929c">90a26350</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-10-23T13:35:15+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>fall back to working ax_with_curses.m4
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/070aa3e4ec96606da81ea2050f351d40cc9de3db">070aa3e4</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-10-23T13:36:03+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>adjust d/changelog
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4dae08be7c8d166e9c8ff48d4c30fd26ecc1c71d">4dae08be</a></strong>
<div>
<span> by Sascha Steinbiss </span> <i> at 2016-10-24T16:33:37+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>dch -r
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0a150351c53793085f7703e85260e6e9d1c93d3a">0a150351</a></strong>
<div>
<span> by Kevin Murray </span> <i> at 2016-11-04T12:08:13+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix usage description of bamshuf/collate
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4b8bdd4adf785df86906d712dda78900f7aa0414">4b8bdd4a</a></strong>
<div>
<span> by John Marshall </span> <i> at 2017-01-05T14:08:54+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Happy New Year
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1bae2510c2f58e0332b84780b3c6bd438c58ed3c">1bae2510</a></strong>
<div>
<span> by John Marshall </span> <i> at 2017-01-09T11:29:31+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Listen to -o FILE option in samtools view -c
Also act on the -o option in is_count mode. Possibly we should use
hopen() instead so arbitrary URLs can be used, but for one %d being
output it seems like fopen() should suffice. Fixes #626.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2b8f06d7375aa40d45f2634ff008389b4be1acf9">2b8f06d7</a></strong>
<div>
<span> by Anton Khodak </span> <i> at 2017-01-12T00:30:46-08:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add CWL tools to the package
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/129288348521ba3ad532d4ba24eb3a5ccb74b703">12928834</a></strong>
<div>
<span> by Anton Khodak </span> <i> at 2017-01-13T06:30:52-08:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add CWL tools
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/11b2ae7173e729dd1a78106482bcea7efadf6706">11b2ae71</a></strong>
<div>
<span> by Anton Khodak </span> <i> at 2017-01-14T09:01:44-08:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>minor fixes
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/861db4215321ed8649dc0f33ebdeb48a989689c4">861db421</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-01-15T10:00:32+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Please use UNRELEASED as long as a package is not uploaded
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0bc88cabb43b1cc43b61acbe7fd0d37531a8dfe6">0bc88cab</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-01-15T10:02:15+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove wrong debian-changes patch
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/30bc5e2dbcbc13ca772a607f5a2fe1cfe12be709">30bc5e2d</a></strong>
<div>
<span> by John Marshall </span> <i> at 2017-01-17T09:12:15+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add the autoconf macros required to the repository
Previously to build from a Git repository developers had to use aclocal
to get these macros from the Autoconf Archive (but release tarballs have
contained an already-built configure script, and will continue to).
This has been a source of user error, and since the following patches
http://git.savannah.gnu.org/cgit/autoconf-archive.git/commit/?id=6dc6cc55a1f3248c8bc39b0abcd5aeb4a3e34a06
http://git.savannah.gnu.org/cgit/autoconf-archive.git/commit/?id=0351b066631215b4fdc3c672a8ef90b233687655
the upstream version of AX_WITH_CURSES barely works and its interface
has been changed (see Debian bug 840974 <https://bugs.debian.org/840974>
comment #35 for details).
Hence we now include copies of autoconf-archive/m4/ax_with_curses.m4 as
at f7dd9928d94cdc780fea4fe17da03f9ccea24891 (serial 15) and serial 1 of
ax_with_htslib.m4 within this repository. It is not ideal to duplicate
external source code within the repository, but they change slowly and
this is now the lesser of two evils.
As an externally-provided ax_with_curses.m4 (in particular) does not
suffice, we've used plain autoconf m4_include rather than an aclocal
approach. (See <https://autotools.io/autoconf/macros.html>.)
README.md recommends `autoconf -Wno-syntax` in order to suppress the
"AC_CONFIG_SUBDIRS: you should use literals" warning. Autoreconf can
also be used, but emits this warning several times.
Fixes #500.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/28a611d2ca71447fc248ff57adf14abbbe3ec7a1">28a611d2</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-01-26T12:40:49+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added multi-threaded decoding to view, index and sort.
These are copied from PR #595 and amalgamated into one commit.
The more contentious parts of that PR or ones not entirely related to
threading have been ditched.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/24971add7fb21e201b5c415b01b69ce9b46042e4">24971add</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-02-09T15:01:20+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Improved multi-threading support for many more samtools commands.
Now BAM has the ability to multi-thread the decoder, and the BAM
encoder threading is more efficient, many sub-commands can now
benefit. For those that already have multi-threading, these have also
migrated to using the sam_opts global option mechanism. (That's still
not an ideal interface, but it suffices for now.)
Sub-commands that have gained -@ or --threads, along with an estimated
speed up from single to 16 threads are:
calmd 5.6
fixmate 12.4
addreplacerg 11.8
collate 1.8
merge 5.0
sort 6.3 (1.4x faster than old 16-way threading)
fastq 1.7
fasta 2.2
view (readonly) 7.8 ("view -f 0xffff" to test decode only)
view (r/w) 12.6 (1.6x faster than old 16-way threading)
flagstat 8.2
index 7.2
split 12.5
Some are still far from ideal as they spend too long in the main
thread doing computation and very little doing decompression and
compression of BAMs. Sub-commands that I didn't try to change or did
but reverted as there is no significant speed benefit include
bedcov, depth, phase, depad, mpileup, targetcut and rmdup along with
various non BAM/CRAM related functions.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/002eb0aaee79cca1159ecafd30fad57d2cad244b">002eb0aa</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2017-02-10T16:17:25+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove redundant item from long options array
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3a7d0f02e8693620014cb59aea17028c5ab427e2">3a7d0f02</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2017-02-10T16:41:39+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update some tests to run both single and multi-threaded
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2e84f7b1d10ad2b04109da9d845697badf85f9ec">2e84f7b1</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2017-02-13T13:41:53+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add MC support to fixmates
Add mate cigar tag support to fixmate and fix tests. (Fixes #170)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9adfa13935715bb7318f5464ba6026703c17430e">9adfa139</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2017-02-13T13:51:03+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add error handling to kstring functions in bam_mate
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e5f5ba1ac7b14dcc9ec802cad1bd3e047bcc9e82">e5f5ba1a</a></strong>
<div>
<span> by Martin O. Pollard </span> <i> at 2017-02-13T14:04:42+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixmates: add tests for two reads unmapped
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d02c177e9195b15d83d0fd486cee0b6d1b71c51d">d02c177e</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2017-02-14T10:25:47+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Temporarily disable the large_chrom bai index test
It doesn't work properly, and gets in the way of fixing the problem
in htslib.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c39caa47a7a262239b99781137c31744f8bb05d1">c39caa47</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-02-20T14:57:41+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Replaced bool with int to avoid confusion with true being failure.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/80ed7c7942ff88d0014bf7a424b527ad36e197ba">80ed7c79</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-02-20T16:42:43+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merged PR#545 (Add MC support to fixmates)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6c4929d29b9d96d7cd74c727265eb08399b87587">6c4929d2</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-02-20T16:43:53+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix to 28a611d2 to prevent samtools view crash on error handling.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/90b0baa524bb09a52d5af6bb9ba453af3f504a7c">90b0baa5</a></strong>
<div>
<span> by Shane McCarthy </span> <i> at 2017-02-23T17:15:01+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>index: update error message for failure to index
After samtools/htslib#470, which fixes the underlying issue #241,
we update the error message upon failure to index. See
https://github.com/samtools/samtools/issues/241#issuecomment-279783955
Closes #241
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/cbee45e4c78a9b155790b5ff1170567bfa6e241f">cbee45e4</a></strong>
<div>
<span> by steveb-cirina </span> <i> at 2017-02-24T13:34:51-08:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fixed a typo: changed "suffices" to "suffixes".</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6587a2b10d0135673a42e0f07c0ae548959773f5">6587a2b1</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2017-03-02T09:08:01+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use htslib_static.mk to get static link flags
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5ec72f173e1e8c4781cd1beec213e63f548b9724">5ec72f17</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-03-02T12:21:13+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Mention multi-threaded BAM/CRAM decoding.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/979bac9b9d655c8b764ed860fb2d761e75a20215">979bac9b</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-03-06T13:41:32+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge branch PR #649 (Use htslib_static.mk to get static link flags)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1bf9afa0cd4a712ac1c087cfc53413638c4ae6cc">1bf9afa0</a></strong>
<div>
<span> by jenniferliddle </span> <i> at 2017-03-06T16:27:11+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Updated with 1.4 changes
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c63b06e054be80fd5d931aab787112a2bafcd8e8">c63b06e0</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2017-03-09T16:49:27+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add liblzma and libbz2 to travis.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3f0407f11728145054a20ce1fc7297cdbf2140e5">3f0407f1</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2017-03-09T21:49:29+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Stop samtools configure from always trying to configure htslib
Add an option --enable-configure-htslib to allow configuration of htslib
to be turned on and off. The default is to only configure htslib when
it is in a subdirectory of samtools (as happens with the distribution
tarballs), and only if --with-htslib=search is used.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e5838c2c12c964baccc914c86cf6456ee4ac648e">e5838c2c</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2017-03-13T10:37:21+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update INSTALL with new library dependencies
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0a859b10a2343f4146fc3c0f71044d182461ad46">0a859b10</a></strong>
<div>
<span> by jenniferliddle </span> <i> at 2017-03-13T14:48:47+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Release 1.4: summary
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a230f81ae489b1023bbf4ebce64ce268683db6ce">a230f81a</a></strong>
<div>
<span> by jenniferliddle </span> <i> at 2017-03-13T14:54:16+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge version number bump and NEWS file from master
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/bda1d8abf284c755a16c68e8feb9541ebab5f153">bda1d8ab</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-03-21T16:23:40+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge tag '1.4' into debian/unstable
Release 1.4 (13 March 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Noteworthy changes in samtools:
* Fixed Issue #345 - out-by-one error in insert-size in samtools stats
* bam_split now add a @PG header to the bam file
* Added mate cigar tag support to fixmate
* Multi-threading is now supported for decoding BAM and CRAM (as well
as the previously supported encoding). Most commands that read BAM
or CRAM have gained an -@ or --threads arguments, providing a
significant speed bonus. For commands that both read and write
files the threads are shared between decoding and encoding tasks.
* Added -a option to samtools mpileup to show all locations, including
sites with zero depth; repeating the option as -aa or -a -a additionally
shows reference sequences without any reads mapped to them (#496).
* The mpileup text output no longer contains empty columns at zero coverage
positions. Previously it would output "...0\t\t..." in some circumstances
(zero coverage due to being below a minumum base quality); this has been
fixed to output as "...0\t*\t*..." with placeholder '*' characters as in
other zero coverage circumstances (see PR #537).
* To stop it from creating too many temporary files, samtools sort
will now not run unless its per-thread memory limit (-m) is set to
at least 1 megabyte (#547).
* The misc/plot-bamstats script now has a -l / --log-y option to change
various graphs to display their Y axis log-scaled. Currently this
affects the Insert Size graph (PR #589; thanks to Anton Kratz).
* Fixmate will now also add and update MC (mate CIGAR) tags.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f83cd5e8518b5a0f838502e2d37e07fc5bdc2e50">f83cd5e8</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-03-21T16:26:52+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Replaced Dominique Belhachemi by my own ID as Uploader
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0dafb696ee61a6fb2a1b9c6bcbceab68283ba307">0dafb696</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-03-21T16:29:23+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Adapt patches
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7e76eb3f5cd98a34b0ad86faccdd1fb78c3ee008">7e76eb3f</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-03-21T19:16:55+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Bump versioned Depends: libhts-dev (>= 1.4), upload to experimental
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/32563cce4ae4e8efbe4270f60d6340c83cf835ce">32563cce</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-03-21T21:43:13+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Rebuild against properly named libhts which had a soname change
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f5120befe07a9bcee844b66fbdc27b59a504b234">f5120bef</a></strong>
<div>
<span> by awenger </span> <i> at 2017-03-22T14:27:05+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add "-b <bam.fofn>" flag to samtools cat.
Add a "-b <bam.fofn>" like that in "samtools merge" to "samtools cat".
This alleviates any problems with the list of input file name exceeding
the number of characters permitted in a single command.
[jkb during merge: adjusted memory freeing and usage format.]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ea2cbba5a88a352d82c390bea6c6c43370aa1f77">ea2cbba5</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-03-22T14:38:42+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Document the "-b bam-list" option to samtools cat.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ea171c4db9969e7a46f4fb58a986541112b6b1a2">ea171c4d</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-03-22T15:09:08+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove two tiny memory leaks in samtools merge.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/692e058392cf9337deac8cbcda74761e73169972">692e0583</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-03-23T11:43:35+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Cram lossy names (#543)
* Added missing input/output options to the man page.
* Rewording of input/output options.
Given the command line options are --input-fmt-options and
--output-fmt-options, it seemed wiser to use the phrases "CRAM input
only" and "CRAM output only" when documenting the input/output option
strings. It still refers to encoding and decoding elsewhere, but I
think this is sufficiently clear.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/86dddab2eaf32207d4ab0df24fb252491e13f5fd">86dddab2</a></strong>
<div>
<span> by Jennifer Liddle </span> <i> at 2017-03-27T16:49:27+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge pull request #560 from george-hall-wtsi/tab_completion
Implemented tab completion</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/90b995fd8fc46f51e39cb8cada14404b828cd2eb">90b995fd</a></strong>
<div>
<span> by Rob Davies </span> <i> at 2017-03-28T15:02:37+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge pull request to enable large vertical movement in tview (#257)
Includes trivial update to replace tabs with spaces.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8c20354dc78540b3a29217945321752a9db4fc52">8c20354d</a></strong>
<div>
<span> by Blaise Li </span> <i> at 2017-03-29T10:10:46+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Option -G to exclude based on a set of bits.
I wanted to be able to exclude reads having a given combination of bits set in
the SAM flag. For instance, to exclude reads where both mates are unmapped, use
`samtools view -G 12`
Did I miss how to do it with -f and -F ?
(Committer: jkb - fixed bam2fq bug to handle -G0 correctly.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b1b6717e7017e5808560b9f808726049f7485f41">b1b6717e</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-03-30T17:33:24+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Improved wording of usage and updated man page.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8b779df31fbcea305923e293070d4e41233070eb">8b779df3</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-03-31T09:49:09+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Another change to view/bam2fq filtering wording.
The previous attempt had "unset" in the wrong place possibly, but it's
now been reworded in terms of flags instead of bits (potentially
permitting the symbolic flag characters again in the future).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/112952092efaa09678470503de751832ba28651f">11295209</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-04-07T09:15:04+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Improvements for C99/XOPEN compliance.
Replaced alloca with malloc.
Avoid arithmetic on void*.
Ensure unsigned types for bit fields.
Use of strings.h for strcasecmp.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/64852009960cb863b598ade1eb74f6bf3c3fa470">64852009</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-04-07T09:15:23+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Switch to -lpthread instead of -pthread for linking.
See https://github.com/samtools/htslib/pull/255 for analogous htslib change.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6d612fea9cb324b15525e172a63270c32420494a">6d612fea</a></strong>
<div>
<span> by jenniferliddle </span> <i> at 2017-04-21T14:35:14+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added option to produce fastq files from BC or other tags
jkb: Removed xstr() and ifmt strdup.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d7b0234d6cd27b790b8bb254d950ba35e277c0fb">d7b0234d</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-04-21T16:57:45+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Output CRAM as temporary sort format iff there are more than 64k cigar ops.
Fixes #667.
In theory we could use CRAM for all temporary output files, but
currently it is too high in memory usage. See the comments included
in this commit for a discussion on how this could be avoided, but for
now we are making the smallest change that fixes the issue as there
are larger issues yet to resolve in sort memory usage.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0aa9fab90bddca2ce277c831ed6407f53cc42496">0aa9fab9</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-04-24T09:27:25+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Bam2fq comment improvements (no code changed).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f13cf4afff4b04fd015bc0512099448d4fd54089">f13cf4af</a></strong>
<div>
<span> by James Bonfield </span> <i> at 2017-05-08T10:47:53+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>NEWS update.
(Ideally merge on day on release, editing date if required.)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8f8600a1e8fbabd7a5a49f307061c3029897a7bc">8f8600a1</a></strong>
<div>
<span> by jenniferliddle </span> <i> at 2017-05-08T11:07:57+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Release 1.4.1: summary
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2ba4095f05d88f8b1cb30977dd75d5109df28122">2ba4095f</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-06-18T21:04:10+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge tag '1.4.1' into debian/unstable
Release 1.4.1 (8th May 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Added options to fastq to create fastq files from BC (or other)
tags.
* Samtools view has gained a -G <flags> option to exclude on all bits
set. For example to discard reads where neither end has been
mapped use "-G 12".
* Samtools cat has a -b <fofn> option to ease concatenation of many
files.
* Added misc/samtools_tab_completion for bash auto-completion of
samtools sub-commands. (#560)
* Samtools tview now has J and K keys for verticale movement by 20
lines. (#257)
* Various compilation / portability improvements.
* Fixed issue with more than 65536 CIGAR operations and SAM/CRAM files.
(#667)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/dd7a11720720b1a1c5ecb5e0598115dec9dce596">dd7a1172</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-06-18T21:07:39+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ae32134425b32940de620ffae81084bf57c1c719">ae321344</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-06-18T21:12:00+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Close bug, upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8a06c510e8e5a19fc0b4115e252b654029642434">8a06c510</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-07-20T12:14:20+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.5</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5eef358408da5e86c3365139744723915ee67d9b">5eef3584</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-07-20T12:14:22+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Updated version 1.5 from '1.5'
with Debian dir 1f9b98601b18347e19cc5281a1b3b962281ce872</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1655d1e2edbade14fa8e81efbdcef96bf66ecaed">1655d1e2</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-07-20T12:15:04+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3092088150ea98f786cd04516d64ceff67066f75">30920881</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-07-20T12:16:28+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>debhelper 10
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d52cd132acd26dd53fd97ddd670c11e6be641268">d52cd132</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-07-20T12:17:05+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Standards-Version: 4.0.0 (no changes needed)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3c0ec5c15af181094f5aca31d65cc589cccd5bda">3c0ec5c1</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-07-20T12:18:15+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Bump versioned Build-Depends: libhts-dev (>= 1.5)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d3b6113420da7dad521d9ce5f53c9a9148b95148">d3b61134</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-08-04T17:58:02+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add recommends to cwl-tool and fix shebang line of cwl scripts
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7f525ad6da62b79b1910f5b44c94a14c064a622a">7f525ad6</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-08-04T18:55:59+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Do not warn about cwl-runner , upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2b7a1c63b1ce8119f6ee576155af7efc39d872d1">2b7a1c63</a></strong>
<div>
<span> by Steffen Moeller </span> <i> at 2017-09-10T11:33:20+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added references to registries
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/007dfe06578db936606dcea62d7fc4081046da0a">007dfe06</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-12-11T15:18:42+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Switch to default Debian Med repository layout
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8abd692651ac07ea7138fe705c83b3253081f3be">8abd6926</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-12-11T15:18:48+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.6</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/eec880f99beffff8a1771c41f9fbc77e6b03285c">eec880f9</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-12-11T15:19:04+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.6'
Update to upstream version '1.6'
with Debian dir 290d6313b34baaaab2f22325cf86f755d204ed21</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9e3a866a0d9dce9deb97789633cf3756b08bdf70">9e3a866a</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-12-11T15:26:51+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Drop literal_version.patch since upstream does not use make to obtain version number any more
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4eb68d19c4416e6130a205efc5c2ff58708e9031">4eb68d19</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-12-11T15:27:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update patches.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6ec08ddc7397fcba353c13b6c91eea89ab1730e6">6ec08ddc</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-12-11T15:29:04+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove deactivated patch
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9a27c5cd56351f18800d78ee7dae7937228f4409">9a27c5cd</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-12-11T15:29:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Standards-Version: 4.1.2
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/18c5fa057cd56de227da814bdbc7197189ff2ac6">18c5fa05</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-12-11T15:34:23+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove unused lintian-overrides
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/938dd3f45d6b969131d49b51d1226a2e16a8dfe3">938dd3f4</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-12-11T15:55:01+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to experimental
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f41c6b342cebe837aeedce9967002382438f15c8">f41c6b34</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-12-11T16:21:27+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Forwarded patch to upstream
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/815e6da09650c9c56de0ac85e0b9e72710a9a6c7">815e6da0</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-12-13T07:44:43+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix versioned Build-Depends
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7649e519334d13c97c17e18f6d0531f7d68c3074">7649e519</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-12-13T08:06:47+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Comment that this was applied upstream
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f722e30b2f8d7780f7e137d94f4164c876d5db7f">f722e30b</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2017-12-14T16:10:28+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/931933e085e8a0d61fd17c1c7e4654a3c9eaffb9">931933e0</a></strong>
<div>
<span> by Graham Inggs </span> <i> at 2017-12-23T09:05:16+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Reduce per-thread memory limit of sort tests, upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d3c6ed11350772e8602efad2643b0b61c5c02f38">d3c6ed11</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-02-14T09:50:25+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.7</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e27e46fba479c06aeefdc8e7d3dfa3dae00552cf">e27e46fb</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-02-14T09:50:51+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.7'
Update to upstream version '1.7'
with Debian dir fe1426d99a1e800c51b64f733eaa53a2119e1b2b</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/77f81d6614429cd5dea04bd4ff5e529269119bf8">77f81d66</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-02-14T09:51:12+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/fffda22fb7a5507cbf49669aa0080a700f266a6d">fffda22f</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-02-14T09:51:42+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Standards-Version: 4.1.3
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8fde52aef53f28113a0cc9c5dc52377830e1fe61">8fde52ae</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-02-14T10:00:06+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>TODO: Adpapt patches
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/619dfea0f5b4ff44b577749fb03287c642d4ddbd">619dfea0</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-02-14T13:21:56+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>adapted patches, mahem patch was applied upstream
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0ac413af581405878760422e2b70ac4e4be94452">0ac413af</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-02-14T13:23:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Bump versioned Build-Depends: libhts-dev (>= 1.7), upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/526f3eeeafb43d7f837df56ff233299b08e5b967">526f3eee</a></strong>
<div>
<span> by Steffen Möller </span> <i> at 2018-03-28T11:23:48+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Updated bio.tools RRID in d/u/metadata</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f2b1311a68e1f5a2d280fe39319024fed6c879d7">f2b1311a</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-03-29T10:00:01+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Install examples (since it is used in dwgsim package and might be helpful for users in general)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d639c0773df6689bbdd0bcb7e17dc26303b18408">d639c077</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-03-29T10:00:01+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>debhelper 11
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a91d8b333596bd61e8de64fdf6e1520b2378cb38">a91d8b33</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-03-29T10:00:01+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d8af890ccd3b960a1b4d022cfeca1254ddffb81f">d8af890c</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-03-29T10:01:41+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove outdated information
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0fddc947cc77f5d5b60622a2f8e9193d43f3f679">0fddc947</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-04-09T14:35:16+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove invalid fields from debian/upstream/metadata
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1452acedf9d260867ea7da5491f16e358201436c">1452aced</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-05-03T12:02:04+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.8</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/cf330a235e2202eed62dd389bda974815e7dd858">cf330a23</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-05-03T12:02:20+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.8'
Update to upstream version '1.8'
with Debian dir c1791e4b4b846627ac181c5e25a26f548469b133</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2cb67ab6de2de68ebfcab02b10dbc447d9aa342c">2cb67ab6</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-05-03T12:02:20+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0ccaa5aedbd5e2f22f91e60139139d6dbfcf2ad8">0ccaa5ae</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-05-03T12:02:23+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/cb2185b40758dc938c626c5143469ad5f734a5db">cb2185b4</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-05-03T12:02:24+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Standards-Version: 4.1.4
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5ff7c75e47964b4ec37adaaef026409f2063a84b">5ff7c75e</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-05-03T13:08:38+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update patches
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e5d95bc9eed9a129dfb582b8b2cea30636589ebd">e5d95bc9</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-05-03T13:15:14+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>hardening=+all
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e2e77e3d04c3a735b74c8d9484c9f9739b7612f8">e2e77e3d</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-05-03T13:16:19+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Bump versioned Build-Depends: libhts-dev (>= 1.8)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1c37793dacc279b726fc5be2e44a888a3943a41f">1c37793d</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-05-03T13:21:28+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to experimental
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7f2247a0e98923d0da621d13e00113a458b149f3">7f2247a0</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2018-05-11T09:44:04+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Mention the CRAM format in the description.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7ad3cb16813792ef1d49c818cc63ce3044b955ec">7ad3cb16</a></strong>
<div>
<span> by Steffen Möller </span> <i> at 2018-05-11T10:20:12+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Updated RRID->SciCrunch in d/u/metadata</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/fc3ddb2b32015ac88b82352460949cd3350a8913">fc3ddb2b</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-09-10T21:34:16+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.9</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c36ba43acf92df200b1117d4e666c71c3abab79d">c36ba43a</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-09-10T21:34:33+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.9'
Update to upstream version '1.9'
with Debian dir 0b13529ef06d0e309f1ddc937c1d412a67d688f7</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d1a74f64676f9f7d87496fa411954f5b1a9c9db0">d1a74f64</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-09-10T22:12:11+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/fb68a4b10dad0f61e8a873e391b8b06c52ea4ff1">fb68a4b1</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-09-10T22:12:49+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Fix Perl interpreter line
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/dd9e496636b2cc4a1365ca0582b72fb561bc98de">dd9e4966</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-09-10T22:14:57+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Standards-Version: 4.2.1
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1ce8831f8153c354161283c0538eaff6ca3224d1">1ce8831f</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2018-09-12T21:48:14+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ede04b46d3e196f8a7dfae48b534599412230ba5">ede04b46</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-01-03T00:21:12-08:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Turn on SSE for i386.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ccfdd9acc39f38b52a936be703c3e56d94606367">ccfdd9ac</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-02-04T08:06:33+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Do not force sse for i386
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6457c973052a5a8470f1789735cb03cfbdafab6e">6457c973</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-02-04T08:06:59+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>debhelper 12
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5063d6b02d9bc28b194446e172cc934cd2386f98">5063d6b0</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-02-04T08:08:28+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c965dae87767a3c88ea444b90d01ba84143f90ec">c965dae8</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-02-04T08:13:11+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/44703ca02abe32314c17cfac82016dff8e80358b">44703ca0</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-02-04T00:19:11-08:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Mark samtools-test as Multi-Arch: foreign.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/770284c73cd785c17e1801ac2e07799c925cdfa0">770284c7</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-02-21T15:34:06+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update debian/README.Debian
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a49f55a448ffcadd7a5fa27f5f8b6cba1b7e0d97">a49f55a4</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-02-21T15:41:21+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Drop reduntant information in debian/reference. It is maintained in debian/upstream/metadata now
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ec29cbbeb8ffc270ca7accfac92a83c96d1dd1f1">ec29cbbe</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-02-21T15:42:24+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Drop invalid comment - we are using canonical layout of git-buildpackage now
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9587f1d14aa3a8ed385c72966c0ed5ec5870046f">9587f1d1</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-02-21T15:59:16+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>install upstream NEWS as upstream changelog
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3c46ee230ac79c35af490627628ca4669e337148">3c46ee23</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-02-21T16:03:11+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>install upstream README as doc
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d1997a0246ab6153410a142663b408e8fec3e0cc">d1997a02</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-02-21T17:45:18+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>more complete debian/NEWS.Debian
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d7024e0e05c7fed2107c4bf8ad80a0ac1e8200ad">d7024e0e</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-02-21T17:55:59+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/26784c71cda38d22a9d7aac2e4ed34df416d34e3">26784c71</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-03-16T18:28:18+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use <!nocheck> for libio-pty-perl
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/73c7856e77eee392b5b338e1d1c15cdb0cb44412">73c7856e</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-08-17T10:19:43+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>drop any-i386
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/16a6a5be2dc531d6b2de6c9353479d63c95bef0b">16a6a5be</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-08-17T10:20:02+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>debhelper-compat 12
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ce17a6c7925a596b2105eb29ebe27a8380648157">ce17a6c7</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-08-17T10:20:05+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/71066ba6126039b4f1e8b79b665027e41a0be4c7">71066ba6</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-08-17T10:21:00+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>release to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5b1c474ae5873ebf1a375fe0d0699dc37d3fe8b8">5b1c474a</a></strong>
<div>
<span> by Steffen Möller </span> <i> at 2019-10-17T16:35:05+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update metadata with ref to conda</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0b80afbb6a271787c6646227e81e2319e6127cf3">0b80afbb</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-12-03T11:45:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Port Python2 script to Python3 using 2to3
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/30c291791df4584a21a2a8805bffeeceba3da926">30c29179</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-12-03T11:45:41+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/909aa9ba67a535c60342197893b9e1e6fd7b7ae3">909aa9ba</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-12-03T11:45:44+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Set fields Upstream-Name in debian/copyright.</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8bf7ff1d4ac22e464b12cdbabf459a1c889804b5">8bf7ff1d</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-12-03T11:45:44+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Set upstream metadata fields: Repository-Browse.</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/82f11d9cac7a15c24bb02b9336e92bc5a8412cc7">82f11d9c</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-12-03T11:45:45+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove obsolete fields Name from debian/upstream/metadata.</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0a09a539872c8501664903b5e9d868bd29635eed">0a09a539</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-12-03T11:50:48+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use python3 dependency once the script was converted
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/49f62d75292e384dc9f7a85d72a27c9ffba030d6">49f62d75</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2019-12-03T11:55:41+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e370503350a23eacacb672d586019854cafcca2f">e3705033</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-12-11T11:01:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Resume building on any as htslib has regained any-i386
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8dac8123352615064ed8d45330e59eee54f51fa0">8dac8123</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-12-11T11:53:06+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.10</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5118a5449307f96a8c7ecc324bb790415cd1516c">5118a544</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-12-11T11:53:32+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.10'
Update to upstream version '1.10'
with Debian dir 82cf39c264dd38e3886be253e11153d597eaaec4</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/556aaa6663f7a23006d90f4d049e228a65a990e1">556aaa66</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-12-11T11:55:32+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>1.10-1
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3ae5e220adfdc88b2e5c957a6cd75c46b571b68c">3ae5e220</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-12-11T11:55:37+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>freshen patches
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/18118746b749878cd2df00951fde4925eacb321e">18118746</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-12-11T11:57:52+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>more build deps
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/76214378d64b2f5bd652ee36c40225cd23c1f5ef">76214378</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-12-16T16:14:17+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>new test path
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d10c1db9d00cd823344ee139c77e5f8c6c7f4be5">d10c1db9</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-12-16T16:17:34+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>1.10-1
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/48bdcecf37aec1f4318d7b8a073a08646cbc0fa1">48bdcecf</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-12-25T14:55:26+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>1.10-2: breaks older iva and bio-tradis
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/02eb5b73e273b7be28ce557a10c051e8e56c9496">02eb5b73</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2019-12-25T17:16:00+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Allow tests to fail on mipsel due to lack of memory
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e8c62ffa10f390937a225fb4188fa9c31510379a">e8c62ffa</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-06-09T11:28:41+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>cwltools only "Suggests" not "Recommends"
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/81ac71e9ddacb88279c35a913c81ba8f5118720a">81ac71e9</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-06-09T11:38:41+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>There are no Python scripts provided in samtools any more
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/95afd029b41fe8420f620c4d4a36dc3bf49a0928">95afd029</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-06-18T22:52:29+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Close bug
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0e522cb483900c65a1458f15ad34a81324a55e01">0e522cb4</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-06-19T11:41:02+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/58200bd8897237e1d3811070f1adc2fe1cc0b242">58200bd8</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-06-19T11:41:02+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/55bc2fb6222bf6b03f6facb62a672f76ba4a7264">55bc2fb6</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-06-19T11:41:20+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ed0a6251d8f434605aeddf9389521461a5538876">ed0a6251</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-06-19T11:41:20+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2077b332650383475a1f5933c28fab0685df5320">2077b332</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-06-19T11:41:39+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a0e76b0805c96ca245c0de5869e5f4035b3122ef">a0e76b08</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-06-19T11:41:40+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Replace use of deprecated $ADTTMP with $AUTOPKGTEST_TMP.
Fixes: lintian: uses-deprecated-adttmp
See-also: https://lintian.debian.org/tags/uses-deprecated-adttmp.html
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ae79f5788c56a890c8582c099b0227e1028e2a9c">ae79f578</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-06-19T11:50:04+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Ready to upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9755953388ff145067ee387d865d5e67aded5b18">97559533</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-10-01T15:54:29+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/eaf4eea97cf035b7f4739d5efb90ce9a258fe967">eaf4eea9</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-10-01T15:54:30+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.11</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/99fb47839174f2705e9ba4070b7f628dfdae2e52">99fb4783</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-10-01T15:54:52+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.11'
Update to upstream version '1.11'
with Debian dir 69670b13b9a616812f79f8edb27ef10387e05d13</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/be2dde947b976eeb48809d855a010f200b6778c7">be2dde94</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-10-01T15:56:33+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Drop spelling patch
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0ca30e0025921f55d45231c836f48f83ec0a8bd4">0ca30e00</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-10-01T16:04:34+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Versioned Build-Depends: libhts-dev (>= 1.11)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/cc518eba11578c569c34adadf811802dc8259f94">cc518eba</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-10-01T16:09:46+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>TODO: Clarify autopkgtest error
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/12b93bb49e98438f86279f9bf5e458039f542be4">12b93bb4</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2020-10-01T16:46:02+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a7be9a5e7302b28e70dbe3559ffa2a2a3ea19f86">a7be9a5e</a></strong>
<div>
<span> by Steffen Möller </span> <i> at 2021-03-06T19:42:50+00:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update metadata - added ref to guix</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/65ce8d200cd98d2ecafe533c1c0123912c7f2f7e">65ce8d20</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-08-27T16:09:51+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/81e41a8bbd49106f5d75627bf433cbedd55b5b01">81e41a8b</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-08-27T16:09:52+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.13</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b807b948372fcea37b401d37f47a1af17080dff0">b807b948</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-08-27T16:10:18+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.13'
Update to upstream version '1.13'
with Debian dir 8a88a12b17a0c6914a92a8b6e80a87a5bb19fbce</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/43491b320a1683564083cf0d720256cebd9f1b01">43491b32</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-08-27T16:10:18+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/56b04e55031bd3167dc8877ee5b8890f2cd0f87a">56b04e55</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-08-27T16:10:22+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/fd8c76141ae1c576ef4762490ca58d165d10b8c1">fd8c7614</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-08-27T16:10:25+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: watch file standard 4
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5c77b324baea8e4971fc77e656e6f3553f20606e">5c77b324</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-08-27T16:13:44+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Ready to upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/11e7fc5f340ba1cac0bd31d8fa10d53fb7077af3">11e7fc5f</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-08-27T16:17:29+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/control: add myself to uploaders
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/85e377eefce55bf6bd675128b8a0c2d7eec33d09">85e377ee</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-08-27T19:13:30+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/control: bump B-D libhts-dev (>= 1.13~)
Attempts to build samtools against older versions are bound to fail,
and will prevent migration to testing of the lot. Thanks Nilesh for
the tip!
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d05af603d52195c4e7ffb025ee091284284fc4ef">d05af603</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-08-27T19:16:41+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>update changelog
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c95b66e8e5b12b0980e9373f9f124eae14cca761">c95b66e8</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2021-08-30T16:32:13+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>make the build reproducible
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/fc228655e35308a3cb76a0ba97ff167edc2a75df">fc228655</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2021-08-30T16:34:55+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Ready to upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/ee4c97ec5b30706383eaa84182e49617125237a3">ee4c97ec</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-10-24T19:24:53+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/rules: fix several issues in manual pages
Most of these were reported by lintian as bad-whatis-entry or
groff-message. Some are still under the radar though.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/488881b3a4b634343d9626646d0f00b469834a91">488881b3</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-10-24T19:29:15+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add fix-ftbfs-mvprintw.patch
Closes: #997180
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d9a875185ab0b58becc2c6b820b141fd95fe8a19">d9a87518</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-10-24T19:35:17+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/rules: prudent pattern to fix whatis entries
Gbp-Dcp: ignore
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/da4dc4aeb3be219b7bfb7b30b186eccb3f828872">da4dc4ae</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-10-24T19:50:10+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/rules: disable executable bit on ac_test.bed
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/fbfd6c99cd3c8e09282a4e9eede187fd014a27f7">fbfd6c99</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-10-24T19:52:33+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add samtools-fasta-q-whatis.patch
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/06566462302cef1fe60d4512228bca03a7941ccd">06566462</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-10-24T19:56:34+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>update changelog
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4cfbf2b48c40ee7aadc39fbdcd9fa8392bf3354b">4cfbf2b4</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-10-24T20:00:08+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/samtools.lintian-overrides removed *.py pattern
Apparently, the samtools do not ship python scripts anymore.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/015d416236770203581849a59c3a8f4f792ab5f4">015d4162</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-10-24T20:28:55+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Adjust fix-ftbfs-mvprintw.patch metainformations
Thanks: John Marshall
This is done in the light of information forwarded upstream and
existing patch with minimum change.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/a35323b79a488fda60725883670bf9fe132dec9b">a35323b7</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-10-24T20:31:11+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>ready to upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/650b7a7fb8a8643305abf7f693021f93318786e9">650b7a7f</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-10-25T00:17:24+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/rules: only disable executable bit if test package is built.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/9c3379035d5b05bd8361a0cfdb47cebc71301b88">9c337903</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-10-25T00:18:53+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>update changelog
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7a4e09b040bb91267a89ab198c0ba3b2cdf21a65">7a4e09b0</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2021-10-25T20:53:12+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>ready for upload to unstable, and close bug
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/d9595e92bbc187b84ebcd6dfb28f5c6672992ac7">d9595e92</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2021-12-07T08:57:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b14cda59ba7d4ec2c45b73ccc2047d482b4dd6bd">b14cda59</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2021-12-07T08:57:23+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.14</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/691f3aa02189a6307d684447cd5e88099fb05e29">691f3aa0</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2021-12-07T08:57:41+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.14'
Update to upstream version '1.14'
with Debian dir 59157f3e7e626bcb67af25eeae86b0c476b7abb6</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b929904f6ac7247bccaf85e69827612ca65e9bcc">b929904f</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2021-12-07T09:12:21+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Cleanup Breaks/Replaces
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/aedf20689471746677359b3f7760d4ca68ac42f4">aedf2068</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2021-12-07T09:12:29+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Refresh patches
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/46030bbf6ef15a85192fba8b5e8499ae1e729c42">46030bbf</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2021-12-07T14:56:30+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to experimental
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f91c2417496ce65cd1ef99a888e0d5f30c0f3406">f91c2417</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2021-12-08T13:20:13+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to experimental
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/af8a82dd0a561d2d721ee469414f70131b48f58e">af8a82dd</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-09-30T11:34:14+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8be6d9fc2cd48c274136707bf9ffe9d51f7dfb92">8be6d9fc</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-09-30T11:34:14+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.16.1</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/bdfbb0049fc0d8051039864d272fa3caf447b986">bdfbb004</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-09-30T11:34:34+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.16.1'
Update to upstream version '1.16.1'
with Debian dir d207ba1f50984d231dfc00fafac4dd2623aeec48</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1964346ec20dbac5ccfd3d82740c2d7054411e38">1964346e</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-09-30T11:34:34+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Standards-Version: 4.6.1
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0cb20ea2d334df54d9fa4d51daf417fb894d18bf">0cb20ea2</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-09-30T11:45:49+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Refresh patches
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e051fd0fcc5b457b2b4b0856105fc35ba919347a">e051fd0f</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-09-30T11:48:56+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f92998e436fe89a4c48ae159320ae51b304ed50b">f92998e4</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-12T20:34:13+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/16dda27071188b068c484d402b3b3aff78911855">16dda270</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-12T20:34:14+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.17</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e038e7229534e04539feb6111428fb60cdc28870">e038e722</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-12T20:34:30+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.17'
Update to upstream version '1.17'
with Debian dir 7083a0de4b9ae81e7003016619b5c4804d76e36c</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/99aa7c6bbbbce9ca071d790f40e9e6dfa3f7fddd">99aa7c6b</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-12T20:34:30+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Standards-Version: 4.6.2
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/aebe148ff605dea27f1cd83c0ad446f6d8b895fa">aebe148f</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-12T20:37:00+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>samtools-fasta-q-whatis.patch: unfuzz
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/dac74908667ed0d469bc9daa5076ab43ad1ef0f7">dac74908</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-12T20:37:15+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/control: clean obsolete package from Breaks:
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5d5421aefa261481e97e525260da7d4ed13aff8c">5d5421ae</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-12T20:38:38+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>update changelog
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/66a6b6e0ae540c9d19db9874933dd273b2ed3c36">66a6b6e0</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-12T20:53:14+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/control: build depends on libhts-dev (>= 1.17~)
Trying to build against older versions will result at best with:
reset.c:107:20: warning: implicit declaration of function ‘bam_aux_first’; did you mean ‘bam_aux_get’? [-Wimplicit-function-declaration]
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/f3e3ea1a954c65a2c2b9fd887aade5fb04bec1d1">f3e3ea1a</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-12T20:54:37+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/control: build depends on libncurses-dev
This replaces the build dependency on libncurses5-dev, which is
flagged as obsolete by lintian.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7adec78675ba7cbea4686b903ef163efdbd3bfce">7adec786</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-12T20:59:35+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/*.lintian-overrides: update mismatched override
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1cc8cf9883be110a933313d336474387820cfcf0">1cc8cf98</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-12T23:27:59+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>update changelog
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/dddb318ee6c6818989a66ce9ba77899f13a910b7">dddb318e</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-18T23:25:58+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>typos.patch: new patch.
This fixes various typos caught by a few of the lintian parsers.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0fd429ba6a0ba10b3661c1ef15209c9422eaed8b">0fd429ba</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-18T23:28:06+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>ready to upload to experimental.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/1efadf4b4aa45b8061e609a895e58f25f165342f">1efadf4b</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-22T22:33:14+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>ready to migrate to unstable.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e756607e32844189008851093d81c25a6a99b5de">e756607e</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-12T21:43:52+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>typos.patch: forwarded upstream.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4d39be10bc70da3172d4208f550f751f5c129922">4d39be10</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-12T21:51:46+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>samtools-fasta-q-whatis.patch: forwarded upstream.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/fd467500f072ad5a71049f03347dd264706e34ba">fd467500</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2023-11-08T07:21:22+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3e070ffd78c060fd5c0d83b60b41b4a8c9063b83">3e070ffd</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2023-11-08T07:21:23+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.18</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c1b903d9bc44d446eeb473c0c4a278f5f90e2ca3">c1b903d9</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2023-11-08T07:21:41+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.18'
Update to upstream version '1.18'
with Debian dir 3484f1d7031e63311a715859da209fd1a4a7e30a</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/71817c1d003f6305230de1723dd6b7a034c4d6c4">71817c1d</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2023-11-08T07:26:58+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove patches applied upstream
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/0a4b8fb8ef1790086a3630b82d765659ba481460">0a4b8fb8</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2023-11-08T09:05:52+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Autopkgtest is now using run-unit-test as user example
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/8c8f2a283c89f39f6dd42c20bd3e0e7578c72085">8c8f2a28</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2023-11-08T09:09:34+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/58f62524d2e1f5414e52346ece12fd89200ecb66">58f62524</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-12-15T16:06:55+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/73082b5feb563379442ff710c06cb5c8dc26c678">73082b5f</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-12-15T16:06:55+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.19</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/73e62d8d4ad5d1d890e9ee4a11cf1e6fc031cbcb">73e62d8d</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-12-15T16:07:12+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.19'
Update to upstream version '1.19'
with Debian dir b967cbff08ac44966a6bd23088b8ca45d645757c</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/b86781db09b5680eb1820ca6b5e95f178a8effbb">b86781db</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-12-15T16:11:51+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/rules: adjust dh_instalchangelogs.
Upstream NEWS file has been renamed NEWS.md.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/66fa6ba6c8d1a1bcfd03d942ab3cd78264632e4f">66fa6ba6</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-12-15T17:36:45+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>ready to upload to unstable.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4ce4e038c3453b1c8ac6a69f60f37e85c254bf46">4ce4e038</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-02-17T18:08:13+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/3f34445e036fd863c877ba8c47fbb5d48a7c9018">3f34445e</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-02-17T18:08:14+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.19.2</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/13ea07afa6ad416117038b1204bc1b73d4db314f">13ea07af</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-02-17T18:08:28+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.19.2'
Update to upstream version '1.19.2'
with Debian dir b891069a499ebe09ea58013b0b6694776a592328</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/e0d4f37ff7f5b822d94530f7c529ff55b223e738">e0d4f37f</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-02-17T18:21:44+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/control: replace pkg-config by pkgconf.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/915b7e32932de046b2cca686e3929d8f4924d7f1">915b7e32</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-02-17T18:22:54+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>ready to upload to unstable.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/6733c3c29832dbcdf207a6f6e0af995135f45f2e">6733c3c2</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-05-29T15:03:06+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.20</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/90a096195e92f3e0a5d64508bedae5e792604636">90a09619</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-05-29T15:03:22+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.20'
Update to upstream version '1.20'
with Debian dir 0c9a8b0c00a6fb58bf78642dea0d042b83beebf6</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/2b57a20334a594f6d69dc7c6f228dc402fc5b6da">2b57a203</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-05-29T15:04:50+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/copyright: update copyright year.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4f1b24240c17aef27d989c398828d86fc08adabe">4f1b2424</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-05-29T15:05:28+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/control: declare compliance to standards version 4.7.0.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/922ea172be6eccb28bd1749b57e0482e101a2a35">922ea172</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-05-29T15:13:39+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/rules: fix permissions of a data file in samtools-test.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/5c53e568f6e30a21e5f8f00377c8fd9b7bbb9952">5c53e568</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-05-29T15:14:22+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>ready for upload to unstable.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/832f44a84283fc9ec76c95269c497efad79a8a6e">832f44a8</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-05-30T20:02:35+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/control: build depends on libhts-dev >= 1.20~.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c2e7702d52d1e7c0de7be82d81489047966c32b3">c2e7702d</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-05-30T20:51:20+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>this upload ended up accepted into unstable.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/56a4a28807a1e729e8cdce70e1ba1fea741e481b">56a4a288</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-05-30T20:51:47+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/rules: fix no-arch-all builds.
The initial issue flown below radar due to leftover htslib version
discrepancy.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/c449bd74c00d8b010d2584ba3d393eb2335408c7">c449bd74</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-05-30T20:53:35+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>ready to upload to unstable.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/4d88bb51aca0935da90cf1c052624837db76f4a3">4d88bb51</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2024-11-14T12:34:54+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.21</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/604c7739765735c2f7af6df3970d5421724f17dd">604c7739</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2024-11-14T12:34:54+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/70892c0f9027184e53b2d6099c1b744da4f22cbf">70892c0f</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2024-11-14T12:35:14+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.21'
Update to upstream version '1.21'
with Debian dir 56313df8ab2a8964f030941dba216a7a5beb6dd6</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/afec661078b4a271110cbde242d0ba87fb54eb85">afec6610</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2024-11-14T17:56:28+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/rules: build-depend on newer htslib 1.21
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/samtools/-/commit/7dc806249b0af0853a95d6c7629e18a04a39c469">7dc80624</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2024-11-14T17:56:28+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Ready to upload to experimental
</pre>
</li>
</ul>
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<a href="#c335a27a082cc8d17dd36dc0eda3086cb0c9baaa">
INSTALL
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<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">
LICENSE
</a>
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<a href="#223d0e76f97df297a3d9662fb77fb71edd34d6f9">
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−
Makefile.mingw
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NEWS
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