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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/2beaa4ed674c5da7f27491f06782596dd3845391">2beaa4ed</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-23T10:00:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/7f44836367952bad93cebe969a6f27f9b706c426">7f448363</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-23T10:14:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forward patches upstream
</pre>
</li>
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<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#62fb7fbdc5102c65487412572090f5a29f2d8966">
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+
debian/bwa-mem2.examples
</span>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#cd30a91f761221230adfef72cc8593b73851bb2e">
<span class="new-file">
+
debian/examples/read1.fq
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<li class="file-stats">
<a href="#301c25f2d3b295d7a829e5588af7cf5c0a3c1805">
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+
debian/examples/read2.fq
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<li class="file-stats">
<a href="#beef0931365c1e9d8f2e2bcb8df8cb67d10df2b6">
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debian/examples/reads.fq
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<li class="file-stats">
<a href="#1d7a126022f228198a91f22bf9f699cd3011238d">
<span class="new-file">
+
debian/examples/ref.fa
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<li class="file-stats">
<a href="#d6c09299b1f914372840e8fd6fcc850f8a11b236">
debian/patches/hardening
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<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
debian/patches/simde
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<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
debian/patches/spelling
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
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debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="62fb7fbdc5102c65487412572090f5a29f2d8966">
<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/18d063f78d51b58c00b69aa2cc5ca8d94abc3abc...7f44836367952bad93cebe969a6f27f9b706c426#62fb7fbdc5102c65487412572090f5a29f2d8966"><strong>debian/bwa-mem2.examples</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">debian/examples/*</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/18d063f78d51b58c00b69aa2cc5ca8d94abc3abc...7f44836367952bad93cebe969a6f27f9b706c426#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bwa-mem2 (2.0-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Add autopkgtests.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> Thu, 23 Jul 2020 09:44:17 +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">bwa-mem2 (2.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Initial release. (Closes: #950607)</span>
</pre>
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</li>
<li id="cd30a91f761221230adfef72cc8593b73851bb2e">
<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/18d063f78d51b58c00b69aa2cc5ca8d94abc3abc...7f44836367952bad93cebe969a6f27f9b706c426#cd30a91f761221230adfef72cc8593b73851bb2e"><strong>debian/examples/read1.fq</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">@HWUSI</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">GTCAGTGAAATCCTGTCTGAACATGGGGGGACCACCCTCC</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">+HWUSI</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhhh</span></pre>
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<li id="301c25f2d3b295d7a829e5588af7cf5c0a3c1805">
<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/18d063f78d51b58c00b69aa2cc5ca8d94abc3abc...7f44836367952bad93cebe969a6f27f9b706c426#301c25f2d3b295d7a829e5588af7cf5c0a3c1805"><strong>debian/examples/read2.fq</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">@HWUSI</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">CGTAGCTGTGTGTACAAGGCCCGGGAACGTATTCACCGTG</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">+HWUSI</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">acdd^aa_Z^d^ddc`^_Q_aaa`_ddc\dfdffff\fff</span></pre>
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<li id="beef0931365c1e9d8f2e2bcb8df8cb67d10df2b6">
<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/18d063f78d51b58c00b69aa2cc5ca8d94abc3abc...7f44836367952bad93cebe969a6f27f9b706c426#beef0931365c1e9d8f2e2bcb8df8cb67d10df2b6"><strong>debian/examples/reads.fq</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">@HWUSI</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">CGTAGCTGTGTGTACAAGGCCCGGGAACGTATTCACCGTG</span>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">+HWUSI</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">acdd^aa_Z^d^ddc`^_Q_aaa`_ddc\dfdffff\fff</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">@HWUSI</span>
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6
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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="LC6" class="line" lang="plaintext">CGTAAATGGACAGCATGACCCGACATCCCACACTCGCCGC</span>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">+HWUSI</span>
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8
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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="LC8" class="line" lang="plaintext">hhhcfhhhhhhhhhhhhghhhhhhffhhhhhhhhhhhhhg</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">@HWUSI</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">AGGGGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCG</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">+HWUSI</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhh</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">@HWUSI</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">GTCAGTGAAATCCTGTCTGAACATGGGGGGACCACCCTCC</span>
</pre>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">+HWUSI</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhhh</span></pre>
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<li id="1d7a126022f228198a91f22bf9f699cd3011238d">
<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/18d063f78d51b58c00b69aa2cc5ca8d94abc3abc...7f44836367952bad93cebe969a6f27f9b706c426#1d7a126022f228198a91f22bf9f699cd3011238d"><strong>debian/examples/ref.fa</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>HWUSI</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">CGTAGCTGTGTGTACAAGGCCCGGGAACGTATTCACCGTG</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">>HWUSI</span>
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4
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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="LC4" class="line" lang="plaintext">CGTAAATGGACAGCATGACCCGACATCCCACACTCGCCGC</span>
</pre>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">>HWUSI</span>
</pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">AGGGGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCG</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">>HWUSI</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">GTCAGTGAAATCCTGTCTGAACATGGGGGGACCACCCTCC</span></pre>
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<li id="d6c09299b1f914372840e8fd6fcc850f8a11b236">
<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/18d063f78d51b58c00b69aa2cc5ca8d94abc3abc...7f44836367952bad93cebe969a6f27f9b706c426#d6c09299b1f914372840e8fd6fcc850f8a11b236"><strong>debian/patches/hardening</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">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="p">Forwarded: https://github.com/bwa-mem2/bwa-mem2/pull/69</span></span>
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<pre style="margin: 0;"> <span id="LC4" 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="LC5" 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="LC6" class="line" lang="diff"><span class="p">@@ -37,7 +37,8 @@</span></span>
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<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/18d063f78d51b58c00b69aa2cc5ca8d94abc3abc...7f44836367952bad93cebe969a6f27f9b706c426#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="p">Forwarded: https://github.com/bwa-mem2/bwa-mem2/pull/84</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- bwa-mem2.orig/src/FMI_search.h</span>
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<pre style="margin: 0;"> <span id="LC6" 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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<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/18d063f78d51b58c00b69aa2cc5ca8d94abc3abc...7f44836367952bad93cebe969a6f27f9b706c426#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</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: fix a typo</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/bwa-mem2/bwa-mem2/pull/83</span></span>
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<pre style="margin: 0;"> <span id="LC4" 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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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bwa-mem2/src/profiling.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -57,7 +57,7 @@</span></span>
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<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/18d063f78d51b58c00b69aa2cc5ca8d94abc3abc...7f44836367952bad93cebe969a6f27f9b706c426#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/18d063f78d51b58c00b69aa2cc5ca8d94abc3abc...7f44836367952bad93cebe969a6f27f9b706c426#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"bwa-mem2"</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell">bwa-mem2 index ref.fa</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">bwa-mem2 mem ref.fa reads.fq <span class="o" style="font-weight: 600;">></span> aln-se.sam </span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">bwa-mem2 mem ref.fa read1.fq read2.fq <span class="o" style="font-weight: 600;">></span> aln-pe.sam </span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span></pre>
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