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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/htslib">Debian Med / htslib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/-/commit/b7f150223972be60323d9c6d3b8890fb7f1b66ef">b7f15022</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-24T07:55:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix description of tabix package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/-/commit/e651026284eb6ab78a37fc155753dd463dc64ae0">e6510262</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-24T07:55:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/-/commit/2543359121e33217b79417078c1903a4d40451f2">25433591</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-12-24T07:55:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update renamed lintian tag names in lintian overrides.
Changes-By: lintian-brush
Fixes: lintian: renamed-tag
See-also: https://lintian.debian.org/tags/renamed-tag.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/-/commit/21425b04d336d9536c137e643816e57ee4295bee">21425b04</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-24T10:28:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Normalise changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/-/commit/c5eda002fe1c8be10d648b37fbccbc72d5a14b6f">c5eda002</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-24T10:34:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Somehow installation of htslib dir has changed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/-/commit/026580eef8faedfc82dd9bc9d0fa900e6201df88">026580ee</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-24T10:41:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#9dc5408ee6e19d2c1f6475ed46a0bf87988c2cc1">
debian/htslib-test.lintian-overrides
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<li class="file-stats">
<a href="#2f5814012a79d3a08214bb3007efa3b3a199233c">
debian/libhts3.install
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/htslib/-/compare/275939091be222aaa6174639481ce0f5059681a7...026580eef8faedfc82dd9bc9d0fa900e6201df88#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.11</span><span class="p">-</span><span class="m" style="color: #099;">3</span><span class="p">)</span> <span class="n" style="color: #333;"><span class="idiff left right">UNRELEASED</span></span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.11</span><span class="p">-</span><span class="m" style="color: #099;">3</span><span class="p">)</span> <span class="n" style="color: #333;"><span class="idiff left right">unstable</span></span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"> <span class="p">[</span> <span class="n" style="color: #333;">Andreas</span> <span class="n" style="color: #333;">Tille</span> <span class="p">]</span></span>
</pre>
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4
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<td class="diff-line-num new_line" data-linenumber="4" 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="LC4" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">No</span> <span class="n" style="color: #333;">need</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">patch</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">proper</span> <span class="n" style="color: #333;">configure</span> <span class="k" style="font-weight: 600;">options</span></span>
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<td class="diff-line-num old_line" data-linenumber="5" 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">
5
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<td class="diff-line-num new_line" data-linenumber="5" 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">
5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Install</span> <span class="n" style="color: #333;">man5</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">user</span> <span class="n" style="color: #333;">rather</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">developer</span> <span class="n" style="color: #333;">documentation</span></span>
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<td class="diff-line-num new old_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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<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="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Fix</span> <span class="n" style="color: #333;">description</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">tabix</span> <span class="k" style="font-weight: 600;">package</span></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="mosel"> <span class="n" style="color: #333;">Closes</span><span class="p">:</span> <span class="p">#</span><span class="m" style="color: #099;">922860</span></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="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.5.1</span> <span class="p">(</span><span class="n" style="color: #333;">routine</span><span class="p">-</span><span class="n" style="color: #333;">update</span><span class="p">)</span></span>
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<td class="diff-line-num new old_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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<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="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Update</span> <span class="n" style="color: #333;">renamed</span> <span class="n" style="color: #333;">lintian</span> <span class="n" style="color: #333;">tag</span> <span class="n" style="color: #333;">names</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lintian</span> <span class="n" style="color: #333;">overrides</span><span class="p">.</span></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="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Somehow</span> <span class="n" style="color: #333;">installation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">htslib</span> <span class="n" style="color: #333;">dir</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">changed</span></span>
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6
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<td class="diff-line-num new_line" data-linenumber="11" 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="LC11" class="line" lang="mosel"></span>
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<td class="diff-line-num old_line" data-linenumber="7" 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="12" 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="LC12" class="line" lang="mosel"> <span class="p">[</span> <span class="n" style="color: #333;">Michael</span> <span class="n" style="color: #333;">R</span><span class="p">.</span> <span class="n" style="color: #333;">Crusoe</span> <span class="p">]</span></span>
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">debian</span><span class="p">/</span><span class="n" style="color: #333;">upstream</span><span class="p">/</span><span class="n" style="color: #333;">metadata</span><span class="p">:</span> <span class="n" style="color: #333;">add</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">pre</span><span class="p">-</span><span class="n" style="color: #333;">print</span></span>
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Andreas</span> <span class="n" style="color: #333;">Tille</span> <span class="p"><</span><span class="n" style="color: #333;">tille</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;"><span class="idiff left">Wed</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">07</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Oct</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2020</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">15</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">06</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">33</span></span><span class="idiff"> </span><span class="p"><span class="idiff">+</span></span><span class="m" style="color: #099;"><span class="idiff right">02</span>00</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Andreas</span> <span class="n" style="color: #333;">Tille</span> <span class="p"><</span><span class="n" style="color: #333;">tille</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;"><span class="idiff left">Thu</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">24</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Dec</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2020</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">10</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">34</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">35</span></span><span class="idiff"> </span><span class="p"><span class="idiff">+</span></span><span class="m" style="color: #099;"><span class="idiff right">01</span>00</span></span>
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11
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="mosel"></span>
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12
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="mosel"><span class="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.11</span><span class="p">-</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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13
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"></span>
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<a href="https://salsa.debian.org/med-team/htslib/-/compare/275939091be222aaa6174639481ce0f5059681a7...026580eef8faedfc82dd9bc9d0fa900e6201df88#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">@@ -14,7 +14,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libssl-dev,</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> libdeflate-dev</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/htslib</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/htslib.git</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Homepage: https://github.com/samtools/htslib</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">@@ -100,4 +100,5 @@ Description: generic indexer for TAB-delimited genome position files</td>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"> chromosomal coordinates. Fast data retrieval also works over network if an URI</span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext"> is given as a file name.</span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> .</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext"> This version of tabix is built from the HTSlib source.</span></pre>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> This package is built from the HTSlib source, and provides the bgzip, htsfile,</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> and tabix tools.</span></pre>
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<a href="https://salsa.debian.org/med-team/htslib/-/compare/275939091be222aaa6174639481ce0f5059681a7...026580eef8faedfc82dd9bc9d0fa900e6201df88#9dc5408ee6e19d2c1f6475ed46a0bf87988c2cc1"><strong>debian/htslib-test.lintian-overrides</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># As needed for testing</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">duplicated-compressed-fil</span>e usr/share/htslib-test/test/bgziptest.txt.gz</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">compressed-duplicat</span>e usr/share/htslib-test/test/bgziptest.txt.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/htslib/-/compare/275939091be222aaa6174639481ce0f5059681a7...026580eef8faedfc82dd9bc9d0fa900e6201df88#2f5814012a79d3a08214bb3007efa3b3a199233c"><strong>debian/libhts3.install</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="php"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/dh-exec</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="no" style="color: #008080;">DEB_HOST_MULTIARCH</span><span class="p">}</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">libhts</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">so</span><span class="mf" style="color: #099;">.</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="no" style="color: #008080;">DEB_HOST_MULTIARCH</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="php"><span class="n" style="color: #333;"><span class="idiff left">usr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">lib</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$</span></span><span class="p"><span class="idiff">{</span></span><span class="no" style="color: #008080;"><span class="idiff">DEB_HOST_MULTIARCH</span></span><span class="p"><span class="idiff">}</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff right">htslib</span></span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="no" style="color: #008080;">DEB_HOST_MULTIARCH</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="n" style="color: #333;"><span class="idiff left">debian</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">tmp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">htslib</span></span><span class="idiff right"> </span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="no" style="color: #008080;">DEB_HOST_MULTIARCH</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"><span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">man</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">man5</span><span class="o" style="font-weight: 600;">/*</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">man</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">man5</span></span></pre>
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