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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcftools">Debian Med / bcftools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcftools/-/commit/f6b9f2e248ba7009e5a26c076a1d259e9865c68d">f6b9f2e2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-17T11:24:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depends on Perl demoted to Recommends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcftools/-/commit/c7d97d8a837d2ecc470d4348d734336f25d8f7dd">c7d97d8a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-17T11:24:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcftools/-/commit/342706c362cfa4dc29160a5757c0a4941285a048">342706c3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-17T11:24:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcftools/-/commit/fe05e7ba37100600c3e661723127d2750181409a">fe05e7ba</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-17T11:24:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcftools/-/commit/18e120296d195b28c8cd1a916c6fdd564272fe9d">18e12029</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-17T11:24:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcftools/-/commit/d27a93df547133ba1c0c0072f1f31a11c5591382">d27a93df</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-17T11:25:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/copyright: use spaces rather than tabs to start continuation lines.
Fixes: lintian: tab-in-license-text
See-also: https://lintian.debian.org/tags/tab-in-license-text.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcftools/-/commit/ef25c900105b6e1e931064080359c7af15c7c0ad">ef25c900</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-17T11:25:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcftools/-/commit/afc04fe752d3a8757ef868ff44e833d63fcf0e43">afc04fe7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-17T11:40:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix Perl recommends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcftools/-/commit/460295209687734c243be802d3052b31241f3896">46029520</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-17T11:46:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Close bug and upload to unstable
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bcftools/-/compare/2448bb187e8c4e5809ddc06b85c3b5c33bededea...460295209687734c243be802d3052b31241f3896#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bcftools (1.10.2-3) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Depends on Perl demoted to Recommends</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #962834</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.5.0 (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * debian/copyright: use spaces rather than tabs to start continuation lines.</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> Repository-Browse.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 17 Jun 2020 11:41:35 +0200</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">bcftools (1.10.2-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> * Fix build on i386 by using SSE2</span>
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<a href="https://salsa.debian.org/med-team/bcftools/-/compare/2448bb187e8c4e5809ddc06b85c3b5c33bededea...460295209687734c243be802d3052b31241f3896#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Michael R. Crusoe <crusoe@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libbz2-dev,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> liblzma-dev,</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,17 +11,18 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libgsl-dev,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> tabix <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libio-pty-perl <!nocheck></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.0</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bcftools</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bcftools.git</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: http://samtools.github.io/bcftools/</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Package: bcftools</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> ${perl:Depends},</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> sse2-support [i386]</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Recommends: perl</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Suggests:</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"># These are needed for plot-vcfstats</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> python,</span>
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<a href="https://salsa.debian.org/med-team/bcftools/-/compare/2448bb187e8c4e5809ddc06b85c3b5c33bededea...460295209687734c243be802d3052b31241f3896#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,17 +4,17 @@ Source: https://github.com/samtools/bcftools</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Copyright:</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> 2011-2015 Genome Research Ltd.</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> 2010-2012 Broad Institute</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><span class="idiff left right"> </span> 2011-2015 Genome Research Ltd.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"><span class="idiff left right"> </span> 2010-2012 Broad Institute</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">License: MIT or GPL-3.0</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Comment:</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> Dual-licensing is in effect for the default compilation mode.</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> When linked with the GPL-licensed GNU Scientific Library</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> (as is done for this Debian package), the</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> resulting program must be distributed under the GPL.</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> The source distribution simply states "GPL-licensed" without indicating</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> a version of the GPL, but includes a copy of GPL-3.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><span class="idiff left right"> </span> Dual-licensing is in effect for the default compilation mode.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"><span class="idiff left right"> </span> When linked with the GPL-licensed GNU Scientific Library</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"><span class="idiff left right"> </span> (as is done for this Debian package), the</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"><span class="idiff left right"> </span> resulting program must be distributed under the GPL.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"><span class="idiff left right"> </span> .</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"><span class="idiff left right"> </span> The source distribution simply states "GPL-licensed" without indicating</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"><span class="idiff left right"> </span> a version of the GPL, but includes a copy of GPL-3.</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Files: kmin.*</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Copyright: 2008,2010 Attractive Chaos <attractor@live.co.uk></span>
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<a href="https://salsa.debian.org/med-team/bcftools/-/compare/2448bb187e8c4e5809ddc06b85c3b5c33bededea...460295209687734c243be802d3052b31241f3896#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcftools/-/compare/2448bb187e8c4e5809ddc06b85c3b5c33bededea...460295209687734c243be802d3052b31241f3896#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Database: https://github.com/samtools/bcftools/issues</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/samtools/bcftools/issues/new</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> - Author: Petr Danecek and Shane A. McCarthy</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Title: ></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,3 +17,5 @@ Registry:</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> Entry: bcftools</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> Entry: bcftools</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Repository: https://github.com/samtools/bcftools.git</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Repository-Browse: https://github.com/samtools/bcftools</span></pre>
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