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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/bwa-mem2">Debian Med / bwa-mem2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/6fc71bf93b0e8ed2660262b1a66c5e0e0da09523">6fc71bf9</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-09T15:46:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update watch file to get complete source tarball
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/6c023326f30a7fa1a139718a9432fb8eac0e267c">6c023326</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-09T16:12:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">improve package hardening
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/136e1c2535604898ddb16de565c561b343f862eb">136e1c25</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-09T16:12:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix a typo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/cde6c0c6e2bc12751da4bc8229b0e068bf8e74ce">cde6c0c6</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-09T16:12:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">enable building on non-x86
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/fe69a7ee423676e3eb7873669598bc4d5f986b25">fe69a7ee</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-09T16:12:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPL code is gone
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/466c9ca17158e513a8419062706b83ef9bf768fe">466c9ca1</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-09T17:14:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">simde fixup
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#d6c09299b1f914372840e8fd6fcc850f8a11b236">
<span class="new-file">
+
debian/patches/hardening
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
</span>
</a>
</li>
<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
<span class="new-file">
+
debian/patches/simde
</span>
</a>
</li>
<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<span class="new-file">
+
debian/patches/spelling
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/7d7ceefbc2e38ab01a92c408892471a342619200...466c9ca17158e513a8419062706b83ef9bf768fe#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,8 @@ Uploaders: Dylan Aïssi <daissi@debian.org>,</td>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> zlib1g-dev</span>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> zlib1g-dev,</span>
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<td class="diff-line-num new old_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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> libsimde-dev</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bwa-mem2</span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bwa-mem2.git</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,10 +14,9 @@ Homepage: https://github.com/bwa-mem2/bwa-mem2</td>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Package: bwa-mem2</span>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Architecture: any<span class="idiff left right">-amd64</span></span>
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<td class="diff-line-num new old_line" data-linenumber="17" 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="17" 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="LC17" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<td class="diff-line-num 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">
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> ${misc:Depends}</span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"># sse4.1-support https://salsa.debian.org/debian/isa-support/merge_requests/1</span>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Description: Sequence alignment using Burrows-Wheeler Transform</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> BWA is a software package for mapping low-divergent sequences against</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> a large reference genome, such as the human genome. It consists of</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/7d7ceefbc2e38ab01a92c408892471a342619200...466c9ca17158e513a8419062706b83ef9bf768fe#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold new_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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ Copyright: 2019 Vasimuddin Md <vasimuddin.md@intel.com></td>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> 2019 Sanchit Misra <sanchit.misra@intel.com></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"> 2019 Intel Corporation</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> 2019 Heng Li <hli@jimmy.harvard.edu></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">License: <span class="idiff left right">GPL-3.0+ and BSD-3-clause</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">License: <span class="idiff left right">Expat</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Files: src/bntseq.*</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> src/bwtindex.cpp</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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="33" 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">@@ -33,7 +33,7 @@ Copyright: 2008 Genome Research Ltd (GRL).</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> 2019 Vasimuddin Md <vasimuddin.md@intel.com></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> 2019 Sanchit Misra <sanchit.misra@intel.com></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> 2019 Intel Corporation</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">License: <span class="idiff left right">GPL-3.0+</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">License: <span class="idiff left right">Expat</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">Comment: There is still reference to previous MIT licence</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">Files: src/kbtree.h</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" 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">@@ -43,6 +43,7 @@ License: BSD-2-Clause</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">Copyright: 2019 Dylan Aïssi <daissi@debian.org></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> 2020 Michael R. Crusoe <crusoe@debian.org></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">License: GPL-3.0+</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">License: BSD-2-Clause</span>
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<li id="d6c09299b1f914372840e8fd6fcc850f8a11b236">
<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/7d7ceefbc2e38ab01a92c408892471a342619200...466c9ca17158e513a8419062706b83ef9bf768fe#d6c09299b1f914372840e8fd6fcc850f8a11b236"><strong>debian/patches/hardening</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Enable proper flag appending so that Debian can harden the build.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bwa-mem2.orig/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bwa-mem2/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -37,7 +37,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> endif </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> ARCH_FLAGS= -msse4.1</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> MEM_FLAGS= -DSAIS=1</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CPPFLAGS= -DENABLE_PREFETCH -DV17=1 $(MEM_FLAGS) </span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ORIG_CPPFLAGS:=$(CPPFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CPPFLAGS+= -DENABLE_PREFETCH -DV17=1 $(MEM_FLAGS) </span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> INCLUDES= -Isrc -Iext/safestringlib/include</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> LIBS= -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> OBJS= src/fastmap.o src/bwtindex.o src/utils.o src/kthread.o \</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -71,14 +72,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> # To provide a different architecture flag like -march=core-avx2.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> ARCH_FLAGS=$(arch)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></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;">-CXXFLAGS= -g -O3 -fpermissive $(ARCH_FLAGS) #-Wall ##-xSSE2</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ORIG_CXXFLAGS:=$(CXXFLAGS)</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;">+CXXFLAGS += -g -O3 -fpermissive $(ARCH_FLAGS) #-Wall ##-xSSE2</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> .PHONY:all clean depend multi</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> .SUFFIXES:.cpp .o</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> .cpp.o:</span>
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<td class="diff-line-num new new_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) -c $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $(INCLUDES) $< -o $@</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> all:$(EXE)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">@@ -89,10 +90,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> $(MAKE) arch=avx2 EXE=bwa-mem2.avx2 CXX=$(CXX) all</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> $(MAKE) arch=avx512 EXE=bwa-mem2.avx512bw CXX=$(CXX) all</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="37" 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="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) -Wall -O3 src/runsimd.cpp -Iext/safestringlib/include -Lext/safestringlib/ -lsafestring -o bwa-mem2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(ORIG_CXXFLAGS) $(ORIG_CPPFLAGS) $(LDFLAGS) -Wall -O3 src/runsimd.cpp -Iext/safestringlib/include -Lext/safestringlib/ -lsafestring -o bwa-mem2</span></span>
</pre>
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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"> $(EXE):$(BWA_LIB) $(SAFE_STR_LIB) src/main.o</span>
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<td class="diff-line-num new new_line" data-linenumber="41" 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="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CXXFLAGS) src/main.o $(BWA_LIB) $(LIBS) -o $@</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) src/main.o $(BWA_LIB) $(LIBS) -o $@</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> $(BWA_LIB):$(OBJS)</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> ar rcs $(BWA_LIB) $(OBJS)</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bwa-mem2.orig/ext/safestringlib/makefile</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bwa-mem2/ext/safestringlib/makefile</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="p">@@ -1,8 +1,8 @@</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> IDIR = include</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> MKDIR_P = mkdir -p</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> CC=gcc</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS=-I$(IDIR) -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LDFLAGS=-z noexecstack -z relo -z now</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS+=-I$(IDIR) -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LDFLAGS+=-z noexecstack -z relo -z now</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> </span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> ODIR=obj</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> OTDIR=objtest</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -30,7 +30,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> $(ODIR)/%.o: $(SRCDIR)/%.c $(DEPS) $(ODEPS)</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;">- $(CC) $(LDFLAGS) -c -o $@ $< $(CFLAGS)</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(CPPFLAGS) $(LDFLAGS) -c -o $@ $< $(CFLAGS)</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> libsafestring.a: $(OBJ)</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> ar rcs $@ $^</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">@@ -44,7 +44,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> $(OTDIR)/%.o: $(TESTDIR)/%.c $(TESTDIR)/test_private.h</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) -c -o $@ $< $(CFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(CPPFLAGS) -c -o $@ $< $(CFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> safestringtest: directories libsafestring.a $(TOBJ)</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/7d7ceefbc2e38ab01a92c408892471a342619200...466c9ca17158e513a8419062706b83ef9bf768fe#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hardening</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">spelling</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">simde</span></pre>
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<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/7d7ceefbc2e38ab01a92c408892471a342619200...466c9ca17158e513a8419062706b83ef9bf768fe#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Enable building on non-x86</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bwa-mem2.orig/src/FMI_search.h</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bwa-mem2/src/FMI_search.h</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -34,7 +34,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> #include <stdlib.h></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> #include <stdint.h></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #include <string.h></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <immintrin.h></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <simde/x86/avx2.h></span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> #include <limits.h></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> #include <fstream></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;">--- bwa-mem2.orig/src/bandedSWA.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;">+++ bwa-mem2/src/bandedSWA.h</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -36,10 +36,17 @@</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> #include <assert.h></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> #include "macro.h"</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </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;">+#if !defined(__SSE__)</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define _mm_malloc(size, align) aligned_alloc(align, size)</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define _mm_free free</span></span>
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24
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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 _MM_HINT_NTA 0</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> #if (__AVX512BW__ || __AVX2__)</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> #include <immintrin.h></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> #else</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <smmintrin.h> // for SSE4.1</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <simde/x86/sse4.1.h> // for SSE4.1</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> #define __mmask8 uint8_t</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> #define __mmask16 uint16_t</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bwa-mem2.orig/src/ksw.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bwa-mem2/src/ksw.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -30,7 +30,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> #include <stdlib.h></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> #include <stdint.h></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> #include <assert.h></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;">-#include <emmintrin.h></span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> #include "ksw.h"</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> #include "macro.h"</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bwa-mem2.orig/src/ksw.h</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bwa-mem2/src/ksw.h</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="p">@@ -26,7 +26,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> #define __AC_KSW_H</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"> #include <stdint.h></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <emmintrin.h></span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</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;">+#include <simde/x86/sse2.h></span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> #define KSW_XBYTE 0x10000</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> #define KSW_XSTOP 0x20000</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bwa-mem2.orig/src/kswv.h</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bwa-mem2/src/kswv.h</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="p">@@ -39,7 +39,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> #include "ksw.h"</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> #include "bandedSWA.h"</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> #else</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;">-#include <immintrin.h></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;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <simde/x86/avx2.h></span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> #endif</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> #ifdef __GNUC__</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;">--- bwa-mem2.orig/src/bwa.h</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bwa-mem2/src/bwa.h</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="p">@@ -37,6 +37,13 @@</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> #include "bwt.h"</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> #include "macro.h"</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> </span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if !defined(__SSE__)</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define _mm_malloc(size, align) aligned_alloc(align, size)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define _mm_free free</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define _MM_HINT_NTA 0</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define _MM_HINT_T0 0</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;">+#endif</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;">+</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> #define BWA_IDX_BWT 0x1</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> #define BWA_IDX_BNS 0x2</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> #define BWA_IDX_PAC 0x4</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bwa-mem2.orig/src/utils.h</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bwa-mem2/src/utils.h</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="p">@@ -63,6 +63,43 @@</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> __asm__ __volatile__ ("rdtsc" : "=a"(lo), "=d"(hi));</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> return ( (unsigned long long)lo)|( ((unsigned long long)hi)<<32 );</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> }</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;">+// From https://github.com/google/benchmark/blob/37177a84b7e8d33696ea1e1854513cb0de3b4dc3/src/cycleclock.h</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Apache 2.0 license</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(__aarch64__)</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // System timer of ARMv8 runs at a different frequency than the CPU's.</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // The frequency is fixed, typically in the range 1-50MHz. It can be</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // read at CNTFRQ special register. We assume the OS has set up</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // the virtual timer properly.</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+static inline unsigned long long __rdtsc(void)</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+{</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;">+ int64_t virtual_timer_value;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ asm volatile("mrs %0, cntvct_el0" : "=r"(virtual_timer_value));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return virtual_timer_value;</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(__ARM_ARCH)</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // V6 is the earliest arch that has a standard cyclecount</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // Native Client validator doesn't allow MRC instructions.</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;">+#if (__ARM_ARCH >= 6)</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;">+static inline unsigned long long __rdtsc(void)</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;">+{</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;">+ uint32_t pmccntr;</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ uint32_t pmuseren;</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ uint32_t pmcntenset;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // Read the user mode perf monitor counter access permissions.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ asm volatile("mrc p15, 0, %0, c9, c14, 0" : "=r"(pmuseren));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="116" 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">
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;">+ if (pmuseren & 1) { // Allows reading perfmon counters for user mode code.</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;">+ asm volatile("mrc p15, 0, %0, c9, c12, 1" : "=r"(pmcntenset));</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;">+ if (pmcntenset & 0x80000000ul) { // Is it counting?</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ asm volatile("mrc p15, 0, %0, c9, c13, 0" : "=r"(pmccntr));</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // The counter is set up to count every 64th cycle</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return static_cast<int64_t>(pmccntr) * 64; // Should optimize to << 6</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</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;">+ struct timeval tv;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ gettimeofday(&tv, nullptr);</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return static_cast<int64_t>(tv.tv_sec) * 1000000 + tv.tv_usec;</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> #endif</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> #endif</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> </span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bwa-mem2.orig/src/fastmap.cpp</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bwa-mem2/src/fastmap.cpp</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="p">@@ -52,7 +52,7 @@</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> #ifdef _WIN32</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> __cpuid((int *) cpuid, (int)i);</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> </span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(__x86_64__) || defined(__i386__)</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> asm volatile</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> ("cpuid" : "=a" (cpuid[0]), "=b" (cpuid[1]), "=c" (cpuid[2]), "=d" (cpuid[3])</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> : "0" (i), "2" (0));</span>
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<td class="diff-line-num new new_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="p">@@ -62,6 +62,7 @@</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> </span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> int HTStatus()</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> {</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if defined(__x86_64__) || defined(__i386__)</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> unsigned int cpuid[4];</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> char platform_vendor[12];</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> __cpuid(0, cpuid);</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="p">@@ -93,6 +94,9 @@</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> fprintf(stderr, "CPUs support hyperThreading !!\n");</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> </span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> return ht;</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#else</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 0;</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> }</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> </span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> </span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bwa-mem2.orig/src/runsimd.cpp</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bwa-mem2/src/runsimd.cpp</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="p">@@ -61,7 +61,7 @@</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> __asm__ volatile ("cpuid"</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> : "=a" (cpuid[0]), "=b" (cpuid[1]), "=c" (cpuid[2]), "=d" (cpuid[3])</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> : "0" (func_id), "2" (subfunc_id));</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else // on 32bit, ebx can NOT be used as PIC code</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(__i386__) // on 32bit, ebx can NOT be used as PIC code</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> __asm__ volatile ("xchgl %%ebx, %1; cpuid; xchgl %%ebx, %1"</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> : "=a" (cpuid[0]), "=r" (cpuid[1]), "=c" (cpuid[2]), "=d" (cpuid[3])</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> : "0" (func_id), "2" (subfunc_id));</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bwa-mem2.orig/src/bwamem.cpp</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bwa-mem2/src/bwamem.cpp</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="p">@@ -1861,7 +1861,7 @@</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> {</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> </span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> int32_t i;</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#if ((!__AVX512BW__) & (__AVX2__ | __SSE2__))</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if (!__AVX512BW__)</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> for(i = 0; i <= MAX_SEQ_LEN16; i++) hist[i] = 0;</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> #else </span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> __m512i zero512 = _mm512_setzero_si512();</span></pre>
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<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/7d7ceefbc2e38ab01a92c408892471a342619200...466c9ca17158e513a8419062706b83ef9bf768fe#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: fix a typo</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bwa-mem2.orig/src/profiling.cpp</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bwa-mem2/src/profiling.cpp</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -57,7 +57,7 @@</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> uint64_t max, min;</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> double avg;</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> fprintf(stderr, "No. of OMP threads: %d\n", nthreads);</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, "Processor is runnig @%lf MHz\n", proc_freq*1.0/1e6);</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, "Processor is running @%lf MHz\n", proc_freq*1.0/1e6);</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> fprintf(stderr, "Runtime profile:\n");</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"> fprintf(stderr, "\n\tTime taken for main_mem function: %0.2lf sec\n\n",</span></pre>
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<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/7d7ceefbc2e38ab01a92c408892471a342619200...466c9ca17158e513a8419062706b83ef9bf768fe#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -2,11 +2,20 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">ifeq (,$(filter $(DEB_HOST_ARCH),amd64 i386))</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">export DEB_CFLAGS_MAINT_APPEND+=-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">export DEB_CXXFLAGS_MAINT_APPEND+=-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> dh_auto_build -- multi</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> dh_auto_build -- ARCH_FLAGS=' '</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"># ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"># dh_auto_build --sourcedir=test -- CXX=g++</span>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/7d7ceefbc2e38ab01a92c408892471a342619200...466c9ca17158e513a8419062706b83ef9bf768fe#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">opts=filenamemangle=s/.+\/v?(\d\S+)\.tar\.gz/bwa-mem2-$1\.tar\.gz/,uversionmangle=s/pre/~pre/ \</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> https://github.com/@PACKAGE@/@PACKAGE@/releases<span class="idiff left right">/latest .*/archive/v?@ANY_VERSION@</span>@ARCHIVE_EXT@</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> https://github.com/@PACKAGE@/@PACKAGE@/releases<span class="idiff left right"> .*/download/v@ANY_VERSION@/Source_code_including_submodule</span>@ARCHIVE_EXT@</span></pre>
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