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<h3>
Michael R. Crusoe 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/103be52531bf6c4303e463ecfff0d5a201f6708c">103be525</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2018-12-11T02:13:22Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try dropping to gcc-7 on i386*
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/commit/c6579182471e49b2877cd575738661e7ca075743">c6579182</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2018-12-18T08:38:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">try suggestion from https://github.com/samtools/htslib/issues/565#issuecomment-448028771
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/commit/112a679b765dda2f1904b3d948203c9786239c1f">112a679b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2018-12-19T15:30:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bring i386 build enhancements to unstable.
</pre>
</li>
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<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>
<li class="file-stats">
<a href="#9dc5408ee6e19d2c1f6475ed46a0bf87988c2cc1">
<span class="new-file">
+
debian/htslib-test.lintian-overrides
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</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/htslib/compare/147dd8065ebf3de7d68827ce34b14c84f5904bad...112a679b765dda2f1904b3d948203c9786239c1f#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;">1.9</span><span class="p">-</span><span class="m" style="color: #099;">7</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="LC2" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Bring</span> <span class="n" style="color: #333;">i386</span> <span class="n" style="color: #333;">build</span> <span class="n" style="color: #333;">enhancements</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">unstable</span><span class="p">.</span></span>
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4
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<pre style="margin: 0;">+<span id="LC5" 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 class="n" style="color: #333;">michael</span><span class="p">.</span><span class="n" style="color: #333;">crusoe</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">></span> <span class="n" style="color: #333;">Wed</span><span class="p">,</span> <span class="m" style="color: #099;">19</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;">30</span><span class="p">:</span><span class="m" style="color: #099;">24</span> <span class="p">-</span><span class="m" style="color: #099;">0800</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">
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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 class="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.9</span><span class="p">-</span><span class="m" style="color: #099;">7</span><span class="p">~</span><span class="m" style="color: #099;">1</span><span class="p">~</span><span class="n" style="color: #333;">i386</span><span class="p">~</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">experimental</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="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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"></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 class="p">*</span> <span class="n" style="color: #333;">Turn</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">SSE</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">i386</span><span class="p">,</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">suggested</span> <span class="n" style="color: #333;">at</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="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">samtools</span><span class="p">/</span><span class="n" style="color: #333;">htslib</span><span class="p">/</span><span class="n" style="color: #333;">issues</span><span class="p">/</span><span class="m" style="color: #099;">565</span><span class="p">#</span><span class="n" style="color: #333;">issuecomment</span><span class="p">-</span><span class="m" style="color: #099;">448028771</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">
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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 class="n" style="color: #333;">michael</span><span class="p">.</span><span class="n" style="color: #333;">crusoe</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">></span> <span class="n" style="color: #333;">Tue</span><span class="p">,</span> <span class="m" style="color: #099;">18</span> <span class="n" style="color: #333;">Dec</span> <span class="m" style="color: #099;">2018</span> <span class="m" style="color: #099;">00</span><span class="p">:</span><span class="m" style="color: #099;">27</span><span class="p">:</span><span class="m" style="color: #099;">40</span> <span class="p">-</span><span class="m" style="color: #099;">0800</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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"></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;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.9</span><span class="p">-</span><span class="m" style="color: #099;">7</span><span class="p">~</span><span class="m" style="color: #099;">0</span><span class="p">~</span><span class="n" style="color: #333;">i386</span><span class="p">~</span><span class="n" style="color: #333;">gcc7</span><span class="p">~</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">experimental</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="15" 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="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;">Try</span> <span class="n" style="color: #333;">dropping</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">gcc</span><span class="p">-</span><span class="m" style="color: #099;">7</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">i386</span><span class="p">*</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC18" 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 class="n" style="color: #333;">michael</span><span class="p">.</span><span class="n" style="color: #333;">crusoe</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">></span> <span class="n" style="color: #333;">Mon</span><span class="p">,</span> <span class="m" style="color: #099;">10</span> <span class="n" style="color: #333;">Dec</span> <span class="m" style="color: #099;">2018</span> <span class="m" style="color: #099;">18</span><span class="p">:</span><span class="m" style="color: #099;">02</span><span class="p">:</span><span class="m" style="color: #099;">16</span> <span class="p">-</span><span class="m" style="color: #099;">0800</span></span>
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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="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.9</span><span class="p">-</span><span class="m" style="color: #099;">6</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="LC21" class="line" lang="mosel"></span>
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3
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<td class="diff-line-num new_line" data-linenumber="22" 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">
22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Revert</span> <span class="n" style="color: #333;">libdeflate</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">DEFLATE</span> <span class="n" style="color: #333;">based</span> <span class="p">(</span><span class="n" style="color: #333;">de</span><span class="p">)</span><span class="n" style="color: #333;">compression</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">crc32</span></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/htslib/compare/147dd8065ebf3de7d68827ce34b14c84f5904bad...112a679b765dda2f1904b3d948203c9786239c1f#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,7 @@ Vcs-Git: https://salsa.debian.org/med-team/htslib.git</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Homepage: https://github.com/samtools/htslib</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Package: libhts2</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Architecture: a<span class="idiff left right">md64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha hppa ia64 kfreebsd-amd64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ny</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Multi-Arch: same</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Section: libs</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,7 +37,7 @@ Description: C library for high-throughput sequencing data formats</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> new index and then for the old if the new index is absent.</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Package: libhts-dev</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">Architecture: a<span class="idiff left right">md64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha hppa ia64 kfreebsd-amd64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ny</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">Multi-Arch: same</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Section: libdevel</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">Depends: libhts2 (= ${binary:Version}),</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">@@ -97,7 +97,7 @@ Description: Test data for HTSlib</td>
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97
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext"> This package contains test files and scripts for the HTSlib.</span>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"></span>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">Package: tabix</span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext">Architecture: a<span class="idiff left right">md64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha hppa ia64 kfreebsd-amd64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ny</span></span>
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101
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> ${shlibs:Depends}</span>
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103
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">Description: generic indexer for TAB-delimited genome position files</span>
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<li id="9dc5408ee6e19d2c1f6475ed46a0bf87988c2cc1">
<a href="https://salsa.debian.org/med-team/htslib/compare/147dd8065ebf3de7d68827ce34b14c84f5904bad...112a679b765dda2f1904b3d948203c9786239c1f#9dc5408ee6e19d2c1f6475ed46a0bf87988c2cc1"><strong>debian/htslib-test.lintian-overrides</strong></a>
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1
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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">duplicated-compressed-file usr/share/htslib-test/test/bgziptest.txt.gz</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/htslib/compare/147dd8065ebf3de7d68827ce34b14c84f5904bad...112a679b765dda2f1904b3d948203c9786239c1f#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" 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">@@ -8,9 +8,9 @@ export DH_VERBOSE=1</td>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386))</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> <span class="idiff left right">export DEB_CFLAGS_MAINT_APPEND=-fno-strict-aliasing -fno-code-hoisting</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> <span class="idiff left right">DEB_CFLAGS_MAINT_APPEND=-msse -mfpmath=sse</span></span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">endif</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">DEB_CFLAGS_MAINT_APPEND+=-flto</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"><span class="idiff left right">export </span>DEB_CFLAGS_MAINT_APPEND+=-flto</span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">export DEB_LDFLAGS_MAINT_APPEND+=-Wl,-flto</span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">%:</span>
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