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<h3>

Michael R. Crusoe pushed to branch master

at <a href="https://salsa.debian.org/med-team/snap-aligner">Debian Med / snap-aligner</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/snap-aligner/-/commit/5c5cd54deac24e0f40f9aee20792094f2b24bcc4">5c5cd54d</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-11-29T08:40:38+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enable building on non-x86 systems via libsimde-dev

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snap-aligner/-/commit/29cb972ae0798e560b5048319431a162047bebba">29cb972a</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-11-29T08:40:39+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/patches/fix_segfault: patch from upstream to fix a segfault I found during testing.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snap-aligner/-/commit/1474a0bbacfa06bc2d247ad2db0ae4f48f3985de">1474a0bb</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-11-29T08:43:43+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">final update to autopkgtest data

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snap-aligner/-/commit/ae172df88e48b64674e77b5523726dd880c4e1ad">ae172df8</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-11-29T08:44:38+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Remove trailing whitespace in debian/control

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snap-aligner/-/commit/a60ea60084197d5573f809a8afda46b706a9ced4">a60ea600</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-11-29T08:45:17+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>7 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#d823bddd2621cf36595a4b621de1b1128134a8a3">

<span class="new-file">

+

debian/patches/fix_segfault.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</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="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

<li class="file-stats">

<a href="#9fe01c87d98ff62c51e222a29eed8f1a830a71a8">

debian/tests/ref/output.sam

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/snap-aligner/-/compare/b69b252998ec93bb3e82f20330f2da75465df0be...a60ea60084197d5573f809a8afda46b706a9ced4#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">snap-aligner (1.0.0+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>

</pre>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">snap-aligner (1.0.0+dfsg-1) <span class="idiff left right">unstable</span>; urgency=medium</span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">  * New upstream version</span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">  * Standards-Version: 4.5.1 (routine-update)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">  * Freshen patches.</span>

</pre>

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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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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">  * debian/docs: Update filename of the manual</span>

</pre>

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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">  * debian/control: try building on s390x and riscv64</span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">    TODO: final autopkgtest segfaults: https://github.com/amplab/snap/issues/129</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">  * Enable building on non-x86 systems via libsimde-dev</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">  * debian/patches/fix_segfault: patch from upstream to fix a segfault I found</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">    during testing.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org>  S<span class="idiff left right">at, 28 Nov 2020 15:36:09</span> +0100</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org>  S<span class="idiff left right">un, 29 Nov 2020 08:44:51</span> +0100</span>

</pre>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">snap-aligner (1.0~beta.18+dfsg-4) unstable; urgency=medium</span>

</pre>

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13

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>

</pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/snap-aligner/-/compare/b69b252998ec93bb3e82f20330f2da75465df0be...a60ea60084197d5573f809a8afda46b706a9ced4#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,7 +6,8 @@ Section: science</td>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>

</pre>

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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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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">               help2man,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" 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">

9

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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC9" class="line" lang="plaintext">               zlib1g-dev</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">               zlib1g-dev,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">               libsimde-dev</span>

</pre>

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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">

10

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Standards-Version: 4.5.1</span>

</pre>

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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">

11

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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">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/snap-aligner</span>

</pre>

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<td class="diff-line-num old_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">

12

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/snap-aligner.git</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,7 +15,7 @@ Homepage: http://snap.cs.berkeley.edu/</td>

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<td class="diff-line-num old_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">

14

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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">Rules-Requires-Root: no</span>

</pre>

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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"></span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Package: snap-aligner</span>

</pre>

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<td class="diff-line-num old old_line" 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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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC17" class="line" lang="plaintext">Architecture: amd64 arm64 mips64el ppc64el s390x alpha kfreebsd-amd64 ppc64 riscv64 sparc64<span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="18" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" 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="LC18" class="line" lang="plaintext">Architecture: amd64 arm64 mips64el ppc64el s390x alpha kfreebsd-amd64 ppc64 riscv64 sparc64</span>

</pre>

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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">Depends: ${shlibs:Depends},</span>

</pre>

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<td class="diff-line-num old_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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<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">         ${misc:Depends}</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="21" 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="LC21" class="line" lang="plaintext">Description: Scalable Nucleotide Alignment Program</span>

</pre>

</td>

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<br>

</li>

<li id="d823bddd2621cf36595a4b621de1b1128134a8a3">

<a href="https://salsa.debian.org/med-team/snap-aligner/-/compare/b69b252998ec93bb3e82f20330f2da75465df0be...a60ea60084197d5573f809a8afda46b706a9ced4#d823bddd2621cf36595a4b621de1b1128134a8a3"><strong>debian/patches/fix_segfault.patch</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From 652076614793f24bbd4f34cb8193269f6661486c Mon Sep 17 00:00:00 2001</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Arun Subramaniyan <sarun2006k1in@gmail.com></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Date: Sat, 28 Nov 2020 16:58:17 -0500</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Subject: [PATCH] Fix segmentation fault when prefetching empty mapped overflow</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> table</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">---</span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> SNAPLib/GenericFile_map.cpp | 9 ++++++++-</span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> 1 file changed, 8 insertions(+), 1 deletion(-)</span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff">diff --git a/SNAPLib/GenericFile_map.cpp b/SNAPLib/GenericFile_map.cpp</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gh" style="color: #999;">index 652e5b9..c789d24 100644</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/SNAPLib/GenericFile_map.cpp</span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/SNAPLib/GenericFile_map.cpp</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -29,6 +29,9 @@</span> Revision History:</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> GenericFile_map *GenericFile_map::open(const char *filename)</span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> {</span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff">  size_t fileSize = QueryFileSize(filename);</span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (0 == fileSize) {</span></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         return new GenericFile_map(NULL, NULL, 0);</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;">+ }</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff">  void *contents;</span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff">  MemoryMappedFile *mappedFile = OpenMemoryMappedFile(filename, 0, fileSize, &contents);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -58,7 +61,11 @@</span> GenericFile_map::~GenericFile_map()</span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff">  _int64</span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> GenericFile_map::prefetch()</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> {</span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    AdviseMemoryMappedFilePrefetch(mappedFile);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (NULL == mappedFile) {</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         return 0;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AdviseMemoryMappedFilePrefetch(mappedFile);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff">  int pageSize = getpagesize();</span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff">  _int64 total = 0;</span></pre>

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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/snap-aligner/-/compare/b69b252998ec93bb3e82f20330f2da75465df0be...a60ea60084197d5573f809a8afda46b706a9ced4#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fix_segfault.patch</span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">non-x86-and-kfreebsd</span>

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">drop-msse</span>

</pre>

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">spelling</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">simde</span></pre>

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<br>

</li>

<li id="4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">

<a href="https://salsa.debian.org/med-team/snap-aligner/-/compare/b69b252998ec93bb3e82f20330f2da75465df0be...a60ea60084197d5573f809a8afda46b706a9ced4#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 systems</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/amplab/snap/pull/130</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;">--- snap-aligner.orig/SNAPLib/Compat.h</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;">+++ snap-aligner/SNAPLib/Compat.h</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -77,12 +77,18 @@</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> #include <sched.h>  // For sched_setaffinity</span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #endif</span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#if defined(__SSE__)  &&  !defined(__APPLE__)</span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <xmmintrin.h>  // This is currently (in Dec 2013) broken on Mac OS X 10.9 (Apple clang-500.2.79)</span></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#define _mm_prefetch(...) {}</span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <emmintrin.h> // For vector types like __m128i</span></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;">-#endif</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;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>

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<pre style="margin: 0;">+<span id="LC17" 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="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if !defined(SIMDE_X86_SSE_NATIVE) && !defined(SIMDE_MATH_SLEEF_ENABLE)</span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+HEDLEY_DIAGNOSTIC_PUSH</span></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  #if HEDLEY_HAS_WARNING("-Wreserved-id-macro")</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="21" 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">

21

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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="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    _Pragma("clang diagnostic ignored \"-Wreserved-id-macro\"")</span></span>

</pre>

</td>

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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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<td class="diff-line-num new new_line" data-linenumber="22" 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">

22

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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="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  #endif</span></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" 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">

23

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#  define _MM_HINT_T0 1</span></span>

</pre>

</td>

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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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<td class="diff-line-num new new_line" data-linenumber="24" 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">

24

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#  define _MM_HINT_T1 2</span></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="25" 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">

25

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#  define _MM_HINT_T2 3</span></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" 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">

26

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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="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+HEDLEY_DIAGNOSTIC_POP</span></span>

</pre>

</td>

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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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<td class="diff-line-num new new_line" data-linenumber="27" 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">

27

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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="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>

</pre>

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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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<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>

</pre>

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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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<td class="diff-line-num new new_line" data-linenumber="29" 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">

29

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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="LC29" class="line" lang="diff"> typedef int64_t _int64;</span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="30" 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">

30

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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="LC30" class="line" lang="diff"> typedef uint64_t _uint64;</span></pre>

</td>

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</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/snap-aligner/-/compare/b69b252998ec93bb3e82f20330f2da75465df0be...a60ea60084197d5573f809a8afda46b706a9ced4#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<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 +5,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all</td>

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5

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>

</pre>

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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">

6

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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">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">VERSION        := $(shell echo $(DEB_VERSION_UPSTREAM) | sed -e 's/+dfsg//')</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<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">

7

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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">

7

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>

</pre>

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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">

8

</td>

<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">export DEB_CXXFLAGS_MAINT_APPEND=-std=gnu++98</span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">export DEB_CXXFLAGS_MAINT_APPEND=-std=gnu++98<span class="idiff left right"> -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP</span></span>

</pre>

</td>

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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">

9

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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">

9

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

</pre>

</td>

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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">

10

</td>

<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">

10

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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">%:</span>

</pre>

</td>

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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">

11

</td>

<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">

11

</td>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">     dh $@</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="9fe01c87d98ff62c51e222a29eed8f1a830a71a8">

<a href="https://salsa.debian.org/med-team/snap-aligner/-/compare/b69b252998ec93bb3e82f20330f2da75465df0be...a60ea60084197d5573f809a8afda46b706a9ced4#9fe01c87d98ff62c51e222a29eed8f1a830a71a8"><strong>debian/tests/ref/output.sam</strong></a>

<hr>

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1

</td>

<td class="diff-line-num new_line" data-linenumber="1" 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">

1

</td>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">@HD   VN:1.4  SO:unsorted</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line" data-linenumber="2" 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">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">@RG   ID:FASTQ        PL:Illumina     PU:pu   LB:lb   SM:sm</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC3" class="line" lang="plaintext">@PG   ID:SNAP PN:SNAP CL:single datatest datatest.fq -o output.sam    VN:1.0<span class="idiff left right">beta.18</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">@PG   ID:SNAP PN:SNAP CL:single datatest datatest.fq -o output.sam    VN:1.0<span class="idiff left right">.0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">@SQ   SN:ref1 LN:202</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">read1 0       ref1    1       70      101M    *       0       0       GTCACAAATGCCACAGAGCAAATGGTCCTGAACAAGCAAACAGAACAGGCCCAGAACACGCCAACCTGTTGAAGACAGAAAGTAGCTTCGTGGCCGGGGGG   -@4>3.>,;$B;A>@&A<<5:@5A?<6<1,>='=7A99=<;7;61></'3+5(<&5,0)30%/=:(&(842&54-+,578)776;.*,&/538)/%$(1,-   PG:Z:SNAP       NM:i:0  RG:Z:FASTQ      PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm</span>

</pre>

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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">

6

</td>

<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">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">read1 0       ref1    102     70      101M    *       0       0       CCACAGCTCTGACTCCTGCATCCTTCTCCTGTGAAGGGGAGGGAGGTGGTGCTGCAGGGGAGGGGAGGGGGCTAGGAGATGTCACTGGGAGCGGAAACGGC   9;6@;:>:2(5.293?+,72$78:974?C>382;A?=:83;96:AB1>=D@4A;C=AD+<E9=;CBC$<EB2@A;BF=EE.FA5>ECE(%FFCDBB1A??F PG:Z:SNAP       NM:i:0  RG:Z:FASTQ      PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm</span></pre>

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