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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/staden-io-lib">Debian Med / staden-io-lib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/staden-io-lib/commit/9ceda5d5316afd2a6867b09283d5361d8332c310">9ceda5d5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-07T06:56:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Apply three patches from upstream to fix bugs on several architectures
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/staden-io-lib/commit/1da454e99a485510a1afc7b5716781515af9d352">1da454e9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-07T07:04:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/staden-io-lib/commit/d49828184c5e15cdfa63478d80a191db3d4dde08">d4982818</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-07T11:53:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix hash table HASH_INT_KEYS on 32-bit platforms
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/staden-io-lib/commit/ac9ba7548ca657996b9a38933a931cc8210e921c">ac9ba754</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-07T11:55:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not attempt to run test suite for architecture independant build.
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#b0e65e4b7cc3388b9c661fece64f58c31859f046">
<span class="new-file">
+
debian/patches/1b28b6a.patch
</span>
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</li>
<li class="file-stats">
<a href="#40ad11de01118b1fdbd89731e2f6737adf1e4a49">
<span class="new-file">
+
debian/patches/242cd6b.patch
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</li>
<li class="file-stats">
<a href="#fca0c3d39adb37f892105dc2bd30e58e387cb775">
<span class="new-file">
+
debian/patches/37b33d3.patch
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</li>
<li class="file-stats">
<a href="#30625f7a3edec3693ddb69d61ad15e688b127b51">
<span class="new-file">
+
debian/patches/d4591b5.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/staden-io-lib/compare/dd8481532c4a66ab2870a5bf82057cc9af0980c6...ac9ba7548ca657996b9a38933a931cc8210e921c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">staden</span><span class="p">-</span><span class="n" style="color: #333;">io</span><span class="p">-</span><span class="n" style="color: #333;">lib</span> <span class="p">(</span><span class="m" style="color: #099;">1.14.11</span><span class="p">-</span><span class="m" style="color: #099;">5</span><span class="p">)</span> <span class="n" style="color: #333;">UNRELEASED</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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<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">
2
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"></span>
</pre>
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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">
3
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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;">Fix</span> <span class="n" style="color: #333;">hash</span> <span class="n" style="color: #333;">table</span> <span class="n" style="color: #333;">HASH_INT_KEYS</span> <span class="n" style="color: #333;">on</span> <span class="m" style="color: #099;">32</span><span class="p">-</span><span class="n" style="color: #333;">bit</span> <span class="n" style="color: #333;">platforms</span> <span class="p">(</span><span class="n" style="color: #333;">thanks</span> <span class="k" style="font-weight: 600;">to</span></span>
</pre>
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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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"> <span class="n" style="color: #333;">upstream</span> <span class="n" style="color: #333;">Rob</span> <span class="n" style="color: #333;">Davies</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="k" style="font-weight: 600;">Do</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">attempt</span> <span class="k" style="font-weight: 600;">to</span> <span class="nf" style="color: #900; font-weight: 600;">run</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">suite</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">architecture</span> <span class="n" style="color: #333;">independant</span></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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="n" style="color: #333;">build</span><span class="p">.</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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"></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;">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;">Fri</span><span class="p">,</span> <span class="m" style="color: #099;">07</span> <span class="n" style="color: #333;">Dec</span> <span class="m" style="color: #099;">2018</span> <span class="m" style="color: #099;">12</span><span class="p">:</span><span class="m" style="color: #099;">52</span><span class="p">:</span><span class="m" style="color: #099;">29</span> <span class="p">+</span><span class="m" style="color: #099;">0100</span></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="mosel"></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="n" style="color: #333;">staden</span><span class="p">-</span><span class="n" style="color: #333;">io</span><span class="p">-</span><span class="n" style="color: #333;">lib</span> <span class="p">(</span><span class="m" style="color: #099;">1.14.11</span><span class="p">-</span><span class="m" style="color: #099;">4</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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<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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Apply</span> <span class="n" style="color: #333;">three</span> <span class="n" style="color: #333;">patches</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">upstream</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">fix</span> <span class="n" style="color: #333;">bugs</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">several</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="mosel"> <span class="n" style="color: #333;">architectures</span> <span class="p">(</span><span class="n" style="color: #333;">thanks</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">lot</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">support</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">James</span> <span class="n" style="color: #333;">Bonfield</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" 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;">915450</span><span class="p">,</span> <span class="p">#</span><span class="m" style="color: #099;">915459</span><span class="p">,</span> <span class="p">#</span><span class="m" style="color: #099;">915460</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC16" 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;">Fri</span><span class="p">,</span> <span class="m" style="color: #099;">07</span> <span class="n" style="color: #333;">Dec</span> <span class="m" style="color: #099;">2018</span> <span class="m" style="color: #099;">07</span><span class="p">:</span><span class="m" style="color: #099;">56</span><span class="p">:</span><span class="m" style="color: #099;">28</span> <span class="p">+</span><span class="m" style="color: #099;">0100</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"><span class="n" style="color: #333;">staden</span><span class="p">-</span><span class="n" style="color: #333;">io</span><span class="p">-</span><span class="n" style="color: #333;">lib</span> <span class="p">(</span><span class="m" style="color: #099;">1.14.11</span><span class="p">-</span><span class="m" style="color: #099;">3</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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2
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Remove</span> <span class="n" style="color: #333;">bashism</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">script</span></span>
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<li id="b0e65e4b7cc3388b9c661fece64f58c31859f046">
<a href="https://salsa.debian.org/med-team/staden-io-lib/compare/dd8481532c4a66ab2870a5bf82057cc9af0980c6...ac9ba7548ca657996b9a38933a931cc8210e921c#b0e65e4b7cc3388b9c661fece64f58c31859f046"><strong>debian/patches/1b28b6a.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: James Bonfield <jkb@sanger.ac.uk></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: Thu, 6 Dec 2018 12:23:53 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Origin: https://github.com/jkbonfield/io_lib/commit/1b28b6a.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/915460</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Subject: [PATCH] Fix rANS codec on x32 architecture.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">This is 32-bit usage of a 64-bit processor. See</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">https://wiki.debian.org/X32Port</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">Should fix the bug found here:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff">https://buildd.debian.org/status/fetch.php?pkg=staden-io-lib&arch=x32&ver=1.14.11-3&stamp=1543952038&raw=0</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> io_lib/rANS_static.c | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> 1 file changed, 1 insertion(+), 1 deletion(-)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/io_lib/rANS_static.c b/io_lib/rANS_static.c</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gh" style="color: #999;">index 4cd6264..e2f64a2 100644</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/io_lib/rANS_static.c</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/io_lib/rANS_static.c</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -339,7 +339,7 @@ static inline void RansDecAdvanceSymbolStep(RansState* r, RansDecSymbol const* s</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> // Renormalize.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __x86_64</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if defined(__x86_64) && !defined(__ILP32__)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> /*</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> * Assembly variants of the RansDecRenorm code.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> * These are based on joint ideas from Rob Davies and from looking at</span></pre>
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<li id="40ad11de01118b1fdbd89731e2f6737adf1e4a49">
<a href="https://salsa.debian.org/med-team/staden-io-lib/compare/dd8481532c4a66ab2870a5bf82057cc9af0980c6...ac9ba7548ca657996b9a38933a931cc8210e921c#40ad11de01118b1fdbd89731e2f6737adf1e4a49"><strong>debian/patches/242cd6b.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Rob Davies <rmd+git@sanger.ac.uk></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: Fri, 7 Dec 2018 11:11:12 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Origin: https://github.com/jkbonfield/io_lib/commit/242cd6b</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/915460</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Subject: [PATCH] Fix hash table HASH_INT_KEYS on 32-bit platforms</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">The hash table has the option to declare the key pointer is the key</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">itself rather than the memory it points to. It assumed however that</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">the key was 8 bytes long, rather than sizeof(char *).</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff">Fixes Debian Bug#915460</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> io_lib/hash_table.c | 10 +++++-----</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> 1 file changed, 5 insertions(+), 5 deletions(-)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/io_lib/hash_table.c b/io_lib/hash_table.c</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gh" style="color: #999;">index 6c37ff8..238cafa 100644</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/io_lib/hash_table.c</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/io_lib/hash_table.c</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -478,7 +478,7 @@ int HashTableResize(HashTable *h, int newsize) {</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> for (hi = h->bucket[i]; hi; hi = next) {</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> uint64_t hv = h2->options & HASH_INT_KEYS</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> ? hash64(h2->options & HASH_FUNC_MASK,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (uint8_t *)&hi->key, hi->key_len) & h2->mask</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (uint8_t *)&hi->key, sizeof(hi->key)) & h2->mask</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> : hash64(h2->options & HASH_FUNC_MASK,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> (uint8_t *)hi->key, hi->key_len) & h2->mask;</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> next = hi->next;</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -535,7 +535,7 @@ HashItem *HashTableAdd(HashTable *h, char *key, int key_len, HashData data,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> key_len = strlen(key);</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> hv = h->options & HASH_INT_KEYS</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ? hash64(h->options & HASH_FUNC_MASK, (uint8_t *)&key, key_len) & h->mask</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ? hash64(h->options & HASH_FUNC_MASK, (uint8_t *)&key, sizeof(key)) & h->mask</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> : hash64(h->options & HASH_FUNC_MASK, (uint8_t *)key, key_len) & h->mask;</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> /* Already exists? */</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -603,7 +603,7 @@ int HashTableDel(HashTable *h, HashItem *hi, int deallocate_data) {</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> hv = h->options & HASH_INT_KEYS</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> ? hash64(h->options & HASH_FUNC_MASK,</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (uint8_t *)&hi->key, hi->key_len) & h->mask</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (uint8_t *)&hi->key, sizeof(hi->key)) & h->mask</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> : hash64(h->options & HASH_FUNC_MASK,</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> (uint8_t *)hi->key, hi->key_len) & h->mask;</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -651,7 +651,7 @@ int HashTableRemove(HashTable *h, char *key, int key_len,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> key_len = strlen(key);</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> hv = h->options & HASH_INT_KEYS</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ? hash64(h->options & HASH_FUNC_MASK, (uint8_t *)&key, key_len) & h->mask</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ? hash64(h->options & HASH_FUNC_MASK, (uint8_t *)&key, sizeof(key)) & h->mask</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> : hash64(h->options & HASH_FUNC_MASK, (uint8_t *)key, key_len) & h->mask;</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> last = NULL;</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -702,7 +702,7 @@ HashItem *HashTableSearch(HashTable *h, char *key, int key_len) {</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> key_len = strlen(key);</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> if (h->options & HASH_INT_KEYS) {</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- hv = hash64(h->options & HASH_FUNC_MASK, (uint8_t *)&key, key_len)& h->mask;</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ hv = hash64(h->options & HASH_FUNC_MASK, (uint8_t *)&key, sizeof(key))& h->mask;</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> for (hi = h->bucket[hv]; hi; hi = hi->next) {</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> if ((int)(size_t)key == (int)(size_t)hi->key)</span></pre>
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<li id="fca0c3d39adb37f892105dc2bd30e58e387cb775">
<a href="https://salsa.debian.org/med-team/staden-io-lib/compare/dd8481532c4a66ab2870a5bf82057cc9af0980c6...ac9ba7548ca657996b9a38933a931cc8210e921c#fca0c3d39adb37f892105dc2bd30e58e387cb775"><strong>debian/patches/37b33d3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: James Bonfield <jkb@sanger.ac.uk></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: Thu, 6 Dec 2018 12:00:39 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Origin: https://github.com/jkbonfield/io_lib/commit/37b33d3.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/915459</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Subject: [PATCH] Bug multi-threaded CRAM decode on some systems.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">The bulk_cram_to_bam function allocated a large array for the BAM</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">objects, but did not ensure the bam structures are aligned on a word</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">boundary. This gave rise to bus errors. Fixes debian Bug#915459</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> io_lib/bam.h | 3 ++-</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> io_lib/cram_decode.c | 9 +++++----</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> 2 files changed, 7 insertions(+), 5 deletions(-)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/io_lib/bam.h</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/io_lib/bam.h</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -271,8 +271,9 @@ static inline void bam_set_bin(bam_seq_t</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> #define bam_qual(b) (bam_seq(b) + (int)(((b)->len+1)/2))</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> #define bam_aux(b) (bam_qual(b) + (b)->len)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-/* Rounds up to the next multiple of 4 */</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/* Rounds up to the next multiple of 4 or 8 */</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> #define round4(v) (((v-1)&~3)+4)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define round8(v) (((v-1)&~7)+8)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> /* CIGAR operations, taken from samtools bam.h */</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> #define BAM_CIGAR_SHIFT 4</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/io_lib/cram_decode.c</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/io_lib/cram_decode.c</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2297,14 +2297,15 @@ static int bulk_cram_to_bam(SAM_hdr *bfd</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> int sz = bam_size(bfd, fd, &s->crecs[i]);</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> if (i < 10000)</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> sizes[i] = sz;</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- len += sz;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ len += round8(sz);</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- s->bl = (bam_seq_t **)malloc(s->hdr->num_records * sizeof(*s->bl) + len);</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ s->bl = (bam_seq_t **)malloc(s->hdr->num_records * sizeof(*s->bl) + len + 8);</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> if (!s->bl)</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> return -1;</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char *x = ((char *)s->bl) + s->hdr->num_records * sizeof(*s->bl);</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // Round up to next multiple of 8, to ensure bam structs are 8-byte aligned.</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char *x = ((char *)s->bl) + round8(s->hdr->num_records * sizeof(*s->bl));</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> for (i = 0; i < s->hdr->num_records; i++) {</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> bam_seq_t *b = (bam_seq_t *)x, *o = b;</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> int bsize = i < 10000 ? sizes[i] : bam_size(bfd, fd, &s->crecs[i]);</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2312,7 +2313,7 @@ static int bulk_cram_to_bam(SAM_hdr *bfd</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> r |= (cram_to_bam(fd->header, fd, s, &s->crecs[i], i, &b) < 0);</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> // if we allocated enough, the above won't have resized b</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> assert(o == b && o->alloc == bsize);</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- x += bsize;</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ x += round8(bsize);</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> s->bl[i] = b;</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span></pre>
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<li id="30625f7a3edec3693ddb69d61ad15e688b127b51">
<a href="https://salsa.debian.org/med-team/staden-io-lib/compare/dd8481532c4a66ab2870a5bf82057cc9af0980c6...ac9ba7548ca657996b9a38933a931cc8210e921c#30625f7a3edec3693ddb69d61ad15e688b127b51"><strong>debian/patches/d4591b5.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: James Bonfield <jkb@sanger.ac.uk></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: Wed, 5 Dec 2018 14:51:09 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Origin: https://github.com/jkbonfield/io_lib/commit/d4591b5.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/915450</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Subject: [PATCH] Big endian fix for BAM reading.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">Fixes Debian Bug#915450</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> io_lib/bam.c | 52 +++++++++++++++++++++++++++-------------------------</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> 1 file changed, 27 insertions(+), 25 deletions(-)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/io_lib/bam.c b/io_lib/bam.c</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gh" style="color: #999;">index 55d0919..b259b50 100644</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/io_lib/bam.c</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/io_lib/bam.c</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -716,7 +716,7 @@ void *bgzf_decode_thread(void *arg) {</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> uint32_t crc1=libdeflate_crc32(0L, (unsigned char *)j->uncomp, j->uncomp_sz);</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> uint32_t crc2;</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> memcpy(&crc2, j->comp + j->comp_sz, 4);</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- crc2 = le_int2(crc2);</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ crc2 = le_int4(crc2);</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> if (crc1 != crc2) {</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> fprintf(stderr, "Invalid CRC in Deflate stream: %08x vs %08x\n",</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> crc1, crc2);</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -754,7 +754,7 @@ void *bgzf_decode_thread(void *arg) {</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> uint32_t crc1=iolib_crc32(0L, (unsigned char *)j->uncomp, s.total_out);</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> uint32_t crc2;</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> memcpy(&crc2, j->comp + j->comp_sz, 4);</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- crc2 = le_int2(crc2);</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ crc2 = le_int4(crc2);</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> if (crc1 != crc2) {</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> fprintf(stderr, "Invalid CRC in Deflate stream: %08x vs %08x\n",</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> crc1, crc2);</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1055,7 +1055,7 @@ static int bam_uncompress_input(bam_file_t *b) {</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> b->uncomp_sz);</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> uint32_t crc2;</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> memcpy(&crc2, b->comp_p-8, 4);</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- crc2 = le_int2(crc2);</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ crc2 = le_int4(crc2);</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> if (crc1 != crc2) {</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> fprintf(stderr, "Invalid CRC in Deflate stream: "</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> "%08x vs %08x\n", crc1, crc2);</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1656,7 +1656,8 @@ static int sam_next_seq(bam_file_t *b, bam_seq_t **bsp) {</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> int bam_get_seq(bam_file_t *b, bam_seq_t **bsp) {</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> int32_t blk_size, blk_ret;</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> bam_seq_t *bs;</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- uint32_t i32;</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ uint32_t u32;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int32_t i32;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> b->line++;</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1701,22 +1702,22 @@ int bam_get_seq(bam_file_t *b, bam_seq_t **bsp) {</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> bs->blk_size = blk_size;</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> bs->ref = le_int4(bs->ref);</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->pos = le_int4(bs->pos_32);</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ i32 = le_int4(bs->pos_32); bs->pos = i32;</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> // order of bit-fields in struct is platform specific, so manually decode</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- i32 = le_int4(bs->bin_packed);</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->bin = i32 >> 16;</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->map_qual = (i32 >> 8) & 0xff;</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->name_len = i32 & 0xff;</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ u32 = le_int4(bs->bin_packed);</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bs->bin = u32 >> 16;</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bs->map_qual = (u32 >> 8) & 0xff;</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bs->name_len = u32 & 0xff;</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- i32 = le_int4(bs->flag_packed);</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->flag = i32 >> 16;</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->cigar_len = i32 & 0xffff;</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ u32 = le_int4(bs->flag_packed);</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bs->flag = u32 >> 16;</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bs->cigar_len = u32 & 0xffff;</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> </span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> bs->len = le_int4(bs->len);</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> bs->mate_ref = le_int4(bs->mate_ref);</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->mate_pos = le_int4(bs->mate_pos_32);</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->ins_size = le_int4(bs->ins_size_32);</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ i32 = le_int4(bs->mate_pos_32); bs->mate_pos = i32;</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ i32 = le_int4(bs->ins_size_32); bs->ins_size = i32;</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> </span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> if (10 == be_int4(10)) {</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> int i, cigar_len = bam_cigar_len(bs);</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1734,7 +1735,8 @@ int bam_get_seq(bam_file_t *b, bam_seq_t **bsp) {</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> int bam_get_seq(bam_file_t *b, bam_seq_t **bsp) {</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> int32_t blk_size, blk_ret;</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> bam_seq_t *bs;</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- uint32_t i32;</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ uint32_t u32;</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int32_t i32;</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> b->line++;</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1769,22 +1771,22 @@ int bam_get_seq(bam_file_t *b, bam_seq_t **bsp) {</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> </span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> bs->blk_size = blk_size;</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> bs->ref = le_int4(bs->ref);</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->pos = le_int4(bs->pos_32);</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ i32 = le_int4(bs->pos_32); bs->pos = i32;</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> // order of bit-fields in struct is platform specific, so manually decode</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- i32 = le_int4(bs->bin_packed);</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->bin = i32 >> 16;</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->map_qual = (i32 >> 8) & 0xff;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->name_len = i32 & 0xff;</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ u32 = le_int4(bs->bin_packed);</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bs->bin = u32 >> 16;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bs->map_qual = (u32 >> 8) & 0xff;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bs->name_len = u32 & 0xff;</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- i32 = le_int4(bs->flag_packed);</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->flag = i32 >> 16;</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->cigar_len = i32 & 0xffff;</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ u32 = le_int4(bs->flag_packed);</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bs->flag = u32 >> 16;</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bs->cigar_len = u32 & 0xffff;</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> </span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> bs->len = le_int4(bs->len);</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> bs->mate_ref = le_int4(bs->mate_ref);</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->mate_pos = le_int4(bs->mate_pos_32);</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bs->ins_size = le_int4(bs->ins_size_32);</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ i32 = le_int4(bs->mate_pos_32); bs->mate_pos = i32;</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ i32 = le_int4(bs->ins_size_32); bs->ins_size = i32;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> </span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> /* Name */</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> if (bam_read(b, &bs->data, bam_name_len(bs)) != bam_name_len(bs))</span></pre>
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<a href="https://salsa.debian.org/med-team/staden-io-lib/compare/dd8481532c4a66ab2870a5bf82057cc9af0980c6...ac9ba7548ca657996b9a38933a931cc8210e921c#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">@@ -2,3 +2,7 @@ pathmax.patch</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_fseeko.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">fix_non_x86.patch</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">remove_bashism.patch</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">d4591b5.patch</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">37b33d3.patch</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">1b28b6a.patch</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">242cd6b.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/staden-io-lib/compare/dd8481532c4a66ab2870a5bf82057cc9af0980c6...ac9ba7548ca657996b9a38933a931cc8210e921c#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" 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>
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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">@@ -35,6 +35,11 @@ override_dh_install-arch:</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> # --version-string="$(version)" \</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> # $(CURDIR)/debian/$(utils)/usr/bin/srf_filter > $(mandir)/srf_filter.1</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">override_dh_install-indep:</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> echo "Do not run test suite for architecture independent builds"</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">override_dh_install-indep:</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> dh_install -i</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> mkdir -p $(testdir)</span>
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