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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bowtie">Debian Med / bowtie</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/-/commit/0c6c1352f43eabdf25cb8325d18536fd9c369fc0">0c6c1352</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-15T08:59:34+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/bowtie/-/commit/8e6c7bb9766e0c8a53c3f52f5a608c9e3bbcb65a">8e6c7bb9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-15T08:59:34+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/bowtie/-/commit/6b2f344de1e2f5457b68ee96a15f0563245110ca">6b2f344d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-15T08:59:44+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.
Changes-By: lintian-brush
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/bowtie/-/commit/a5c817953630cb1b06c30c77b4f9a03751638772">a5c81795</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-15T09:06:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Seems seqan-rename-ChunkPool.patch was not finished since there is a build error
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/-/commit/56a58b4d186c5cfe568a6571b9104a25c04c28f5">56a58b4d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-15T09:19:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop seqan-dev from Build-Depends and deactivate patch to rename ChunkPool and popCount from seqan
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/-/commit/b63942ffcfc1cdcd12e6b47fcecdbf1c97df9b64">b63942ff</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-15T09:38:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point dh_install to binaries available in usr/local/bin
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/-/commit/eda38d7a4a769e331c0eb6aa185c3c91bc0f4512">eda38d7a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-15T09:49:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Also install -debug version of the binaries since these were in previous packages as well ... but why????
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/-/commit/8dc9e138ac757d83873085e78c9985d951d8b288">8dc9e138</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-15T09:58:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#43569291b6bbd69617b7b06790834d98fe79040f">
debian/bowtie.install
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#f538a565cba7a15bfc8a566b008158b7820facdd">
debian/patches/seqan-rename-ChunkPool.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</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="43569291b6bbd69617b7b06790834d98fe79040f">
<a href="https://salsa.debian.org/med-team/bowtie/-/compare/5944e054c3300c591655f0f33534952438cf10e6...8dc9e138ac757d83873085e78c9985d951d8b288#43569291b6bbd69617b7b06790834d98fe79040f"><strong>debian/bowtie.install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">bowtie</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="php"><span class="nx">bowtie</span><span class="o" style="font-weight: 600;">-</span><span class="nx">align</span><span class="o" style="font-weight: 600;">*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="php"><span class="nx">bowtie</span><span class="o" style="font-weight: 600;">-</span><span class="nx">build</span><span class="o" style="font-weight: 600;">*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="php"><span class="nx">bowtie</span><span class="o" style="font-weight: 600;">-</span><span class="nx">inspect</span><span class="o" style="font-weight: 600;">*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">local</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span> <span class="nx">usr</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tests</span><span class="o" style="font-weight: 600;">/</span><span class="p">[</span><span class="nx">er</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bowtie</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tests</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="nx">bowtie</span><span class="o" style="font-weight: 600;">-*-</span><span class="nx">debug</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
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<br>
</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bowtie/-/compare/5944e054c3300c591655f0f33534952438cf10e6...8dc9e138ac757d83873085e78c9985d951d8b288#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">bowtie (1.3.0+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bowtie (1.3.0+dfsg-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * New upstream version (upstream has adopted several patches)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.5.0 (routine-update)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 15 Sep 2020 08:16:20 +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Repository-Browse.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Drop seqan-dev from Build-Depends</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Point dh_install to binaries available in usr/local/bin</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 15 Sep 2020 09:50:29 +0200</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">bowtie (1.2.3+dfsg-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bowtie/-/compare/5944e054c3300c591655f0f33534952438cf10e6...8dc9e138ac757d83873085e78c9985d951d8b288#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">@@ -11,7 +11,6 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> help2man,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libtbb-dev,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> seqan-dev,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libclone-perl,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> libtest-deep-perl,</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">@@ -20,6 +19,7 @@ Standards-Version: 4.5.0</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bowtie</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bowtie.git</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Homepage: http://bowtie-bio.sourceforge.net/</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Package: bowtie</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Architecture: alpha any-amd64 arm64 mips64el ppc64 ppc64el s390x sparc64 riscv64</span>
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<li id="f538a565cba7a15bfc8a566b008158b7820facdd">
<a href="https://salsa.debian.org/med-team/bowtie/-/compare/5944e054c3300c591655f0f33534952438cf10e6...8dc9e138ac757d83873085e78c9985d951d8b288#f538a565cba7a15bfc8a566b008158b7820facdd"><strong>debian/patches/seqan-rename-ChunkPool.patch</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">@@ -140,6 +140,15 @@ Last-Update: 2013-04-18</td>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="diff"> BitPairReference* refs,</span>
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="diff"> EList<BTRefString >& os,</span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="diff"> bool maqPenalty,</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="p">@@ -597,7 +597,7 @@</span> public:</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> RangeCache* cacheFw,</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> RangeCache* cacheBw,</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> uint32_t cacheLimit,</span>
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<td class="diff-line-num new new_line" data-linenumber="147" 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="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ChunkPool *pool,</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bowtieChunkPool *pool,</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> BitPairReference* refs,</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> EList<BTRefString >& os,</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> bool reportSe,</span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="diff"><span class="p">@@ -1372,7 +1372,7 @@</span> private:</span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="diff"> RangeCache *cacheFw_;</span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="diff"> RangeCache *cacheBw_;</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/bowtie/-/compare/5944e054c3300c591655f0f33534952438cf10e6...8dc9e138ac757d83873085e78c9985d951d8b288#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -3,8 +3,8 @@ strip_html5shiv.patch</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">spelling.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">no_hash_style_both_for_mips.patch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">use-dpkg-buildflags.patch</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">seqan-rename-ChunkPool.patch</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">seqan-popcount.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><span class="idiff left right"># </span>seqan-rename-ChunkPool.patch</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><span class="idiff left right"># </span>seqan-popcount.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">reproducible.patch</span>
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<td class="diff-line-num old_line" data-linenumber="9" 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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<td class="diff-line-num new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext">build-as-Cpp03.patch</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">simple-test</span></pre>
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<li id="b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<a href="https://salsa.debian.org/med-team/bowtie/-/compare/5944e054c3300c591655f0f33534952438cf10e6...8dc9e138ac757d83873085e78c9985d951d8b288#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/bowtie/-/compare/5944e054c3300c591655f0f33534952438cf10e6...8dc9e138ac757d83873085e78c9985d951d8b288#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/BenLangmead/bowtie/issues</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/BenLangmead/bowtie/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: "Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg\n"</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> title: "Ultrafast and memory-efficient alignment of short DNA sequences to the human\</span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" 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">@@ -18,3 +20,5 @@ Registry:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> Entry: bowtie</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">- Name: conda:bioconda</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> Entry: bowtie</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Repository: https://github.com/BenLangmead/bowtie.git</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Repository-Browse: https://github.com/BenLangmead/bowtie</span></pre>
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