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GitLab

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<h3>

Michael R. Crusoe pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/abyss/commit/5665d58614446040139fc1940780f2a5fdf8db22">5665d586</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-09-28T08:22:24Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/abyss/commit/2fd2fcae006d896842a0964075c44fca4a615324">2fd2fcae</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-09-28T08:22:25Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.2.3</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/abyss/commit/40cef023ddc1e056a92b2adb5cf358d49ca1604b">40cef023</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-09-28T08:22:27Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.2.3'

Update to upstream version '2.2.3'

with Debian dir aa97618ff0085c98603f3de5b5cfbcca5423a3a4</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/abyss/commit/37037f506842af3af681a5572fa96a6a3c5d7d26">37037f50</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-09-28T08:33:35Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove strict-alignment patch as per upstream

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/abyss/commit/da98c1f869bdf53fac40098ae271ea00de1a6102">da98c1f8</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-09-28T08:33:49Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">spelling patch has been forwarded to upstream

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/abyss/commit/3e835742f42708d5c11472c9170cdafe64fc509c">3e835742</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-09-28T08:39:28Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">upstream has fixed the g++9 warnings problem

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/abyss/commit/c3087b6aca42cca9614afeb6df63ef9b2a9078f6">c3087b6a</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-09-28T08:39:28Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">try without 32bit patch

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/abyss/commit/a3f928f99577bb66c920920def6528fb74faf572">a3f928f9</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-09-28T10:05:16Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">release 2.2.3-1

</pre>

</li>

</ul>

<h4>19 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#a56cf4a4d7916a36bb673587cdcc147c0f71ec4e">

BloomDBG/bloom-dbg.cc

</a>

</li>

<li class="file-stats">

<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">

ChangeLog

</a>

</li>

<li class="file-stats">

<a href="#74c12a339404c9414a46b07e63f28cc87c8355bd">

Common/ContigNode.h

</a>

</li>

<li class="file-stats">

<a href="#844825323b2e1e9112e4140819049dd37caf73ee">

Graph/ContigGraph.h

</a>

</li>

<li class="file-stats">

<a href="#610175bbb054337b678fdcf4fb5eb7a7b40d31e6">

Graph/DirectedGraph.h

</a>

</li>

<li class="file-stats">

<a href="#cc89e9bae60f4855d94b92272217e92ebb5bcf52">

Misc/samtobreak.hs

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#e9d1fc75e09569c2f720b16b5ad725181dd43d69">

Unittest/BloomDBG/CountingBloomFilterTest.cpp

</a>

</li>

<li class="file-stats">

<a href="#40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4">

azure-pipelines.yml

</a>

</li>

<li class="file-stats">

<a href="#cd06d399cbb97ac80091363ace10b558e194af5f">

bin/abyss-pe

</a>

</li>

<li class="file-stats">

<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">

configure.ac

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">

debian/patches/spelling

</a>

</li>

<li class="file-stats">

<a href="#6091197197b5b3ed653a0d23955ce03d57fb83d3">

<span class="deleted-file">

−

debian/patches/strict_alignment.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

<li class="file-stats">

<a href="#54545de904c655f7c6b1ed6e0f6e947540dbf202">

doc/ABYSS.1

</a>

</li>

<li class="file-stats">

<a href="#210a6761e540ac8179e4a92fdffba66759a77e27">

doc/abyss-pe.1

</a>

</li>

<li class="file-stats">

<a href="#58b9c1ec4a434e1b73496c894a35770e972461a5">

doc/abyss-tofastq.1

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="a56cf4a4d7916a36bb673587cdcc147c0f71ec4e">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#a56cf4a4d7916a36bb673587cdcc147c0f71ec4e"><strong>BloomDBG/bloom-dbg.cc</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="357" 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="357" 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">@@ -357,11 +357,14 @@ countingBloomAssembly(int argc, char** argv, const BloomDBG::AssemblyParams& par</td>

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

<td class="diff-line-num old_line" data-linenumber="357" 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">

357

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<td class="diff-line-num new_line" data-linenumber="357" 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">

357

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp">          <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">params</span><span class="p">;</span></span>

</pre>

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

<td class="diff-line-num old_line" data-linenumber="358" 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">

358

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<td class="diff-line-num new_line" data-linenumber="358" 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">

358

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

<pre style="margin: 0;"> <span id="LC358" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="359" 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">

359

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<td class="diff-line-num new_line" data-linenumber="359" 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">

359

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

<pre style="margin: 0;"> <span id="LC359" class="line" lang="cpp">  <span class="cm" style="color: #998; font-style: italic;">/* Initialize a counting Bloom filter:</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="360" 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">

360

</td>

<td class="diff-line-num new_line old" data-linenumber="360" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC360" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">         Divide the requested memory in bytes by the byte-size of each counter to determine the number</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="361" 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">

361

</td>

<td class="diff-line-num new_line old" data-linenumber="360" 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="LC361" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">         of counters, and then round up that count to the next multiple of 64.*/</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="362" 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="360" 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">

360

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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="LC360" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">         Divide the requested memory in bytes by 1.125 to account for the memory used</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="362" 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="361" 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">

361

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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="LC361" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">         in building the visitedKmer BloomFilter. Then further divide the byte-size</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="362" 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="362" 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="LC362" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">         of each counter to determine the number of counters, and then round up that</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="362" 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="363" 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="LC363" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">         count to the next multiple of 64.*/</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="362" 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">

362

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<td class="diff-line-num new_line" data-linenumber="364" 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">

364

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

<pre style="margin: 0;"> <span id="LC364" class="line" lang="cpp"></span>

</pre>

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

<td class="diff-line-num new old_line" data-linenumber="363" 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="365" 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">

365

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">countingBloomFilterSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">bloomSize</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">1.125</span> <span class="o" style="font-weight: 600;">/</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">BloomCounterType</span><span class="p">);</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">counters</span> <span class="o" style="font-weight: 600;">=</span></span>

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<pre style="margin: 0;">-<span id="LC364" class="line" lang="cpp">      <span class="n" style="color: #333;">BloomDBG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">roundUpToMultiple</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">params</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bloomSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">BloomCounterTyp</span>e</span><span class="p">),</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="mi" style="color: #099;">64</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp">      <span class="n" style="color: #333;">BloomDBG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">roundUpToMultiple</span><span class="p">(<span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">round</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">countingBloomFilterSiz</span>e</span><span class="p">),</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="mi" style="color: #099;">64</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="cpp">  <span class="n" style="color: #333;">CountingBloomFilterType</span> <span class="n" style="color: #333;">bloom</span><span class="p">(</span><span class="n" style="color: #333;">counters</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">numHashes</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">minCov</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp"></span>

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<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2019-09-20  Johnathan Wong <jowong@bcgsc.ca></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">      * Release version 2.2.3</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">      * Revert memory consumption of Bloom filters to pre 2.2.0 behaviour</span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">      ABySS will now share the specified memory among all Bloom filters</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">      instead of just the counting Bloom filter.</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">      * Fix gcc-9 compilation warnings</span>

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">2019-08-16  Johnathan Wong <jowong@bcgsc.ca></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">     * Release version 2.2.2</span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +19,7 @@</td>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">2019-08-01  Johnathan Wong <jowong@bcgsc.ca></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">     * Release version 2.2.0</span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">     * Construct a counting <span class="idiff left right">bloom filter instead of a cascading b</span>loom filter.</span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">     * Construct a counting <span class="idiff left right">Bloom filter instead of a cascading B</span>loom filter.</span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">     abyss-bloom:</span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">     * Add 'counting' as valid argument to '-t' option to build a counting</span>

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<li id="74c12a339404c9414a46b07e63f28cc87c8355bd">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#74c12a339404c9414a46b07e63f28cc87c8355bd"><strong>Common/ContigNode.h</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">@@ -69,6 +69,11 @@ ContigNode operator^(bool sense) const</td>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c">     <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ContigNode</span><span class="p">(</span><span class="n" style="color: #333;">m_index</span> <span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">sense</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Copy constructors */</span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"><span class="n" style="color: #333;">ContigNode</span><span class="p">(</span><span class="n" style="color: #333;">ContigNode</span><span class="o" style="font-weight: 600;">&&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"><span class="n" style="color: #333;">ContigNode</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ContigNode</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"><span class="n" style="color: #333;">ContigNode</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">ContigNode</span><span class="o" style="font-weight: 600;">&&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Return whether this ContigNode is ambiguous. */</span></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">ambiguous</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c"><span class="p">{</span></span>

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<li id="844825323b2e1e9112e4140819049dd37caf73ee">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#844825323b2e1e9112e4140819049dd37caf73ee"><strong>Graph/ContigGraph.h</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">@@ -15,6 +15,13 @@ using boost::graph_traits;</td>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c"><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">ContigGraph</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">G</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c">  <span class="nl">public:</span></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c">     <span class="cm" style="color: #998; font-style: italic;">/** Copy constructors */</span></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c">     <span class="n" style="color: #333;">ContigGraph</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ContigGraph</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c">     <span class="n" style="color: #333;">ContigGraph</span><span class="p">(</span><span class="n" style="color: #333;">ContigGraph</span><span class="o" style="font-weight: 600;">&&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c">     <span class="n" style="color: #333;">ContigGraph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ContigGraph</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c">     <span class="n" style="color: #333;">ContigGraph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">ContigGraph</span><span class="o" style="font-weight: 600;">&&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c">     <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">G</span> <span class="n" style="color: #333;">base_type</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c">     <span class="c1" style="color: #998; font-style: italic;">// Graph</span></span>

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</li>

<li id="610175bbb054337b678fdcf4fb5eb7a7b40d31e6">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#610175bbb054337b678fdcf4fb5eb7a7b40d31e6"><strong>Graph/DirectedGraph.h</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">@@ -545,8 +545,15 @@ class Edge</td>

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="c">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ui</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m_removed</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">m_removed</span><span class="p">[</span><span class="n" style="color: #333;">ui</span><span class="p">]</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC546" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC547" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC548" class="line" lang="c">  <span class="nl">protected:</span></span>

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<pre style="margin: 0;">+<span id="LC549" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC550" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/** Copy constructors */</span></span>

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="c">    <span class="n" style="color: #333;">DirectedGraph</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">DirectedGraph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">d</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC552" class="line" lang="c">    <span class="n" style="color: #333;">DirectedGraph</span><span class="p">(</span><span class="n" style="color: #333;">DirectedGraph</span><span class="o" style="font-weight: 600;">&&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC553" class="line" lang="c">    <span class="n" style="color: #333;">DirectedGraph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">DirectedGraph</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="c">    <span class="n" style="color: #333;">DirectedGraph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">DirectedGraph</span><span class="o" style="font-weight: 600;">&&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC555" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC556" class="line" lang="c">  <span class="nl">private:</span></span>

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<pre style="margin: 0;">-<span id="LC549" class="line" lang="c">    <span class="n" style="color: #333;">DirectedGraph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">operator</span> <span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">DirectedGraph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="c"></span>

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<td class="diff-line-num new_line" data-linenumber="558" 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="LC558" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/** The set of vertices. */</span></span>

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<td class="diff-line-num new_line" data-linenumber="559" 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="LC559" class="line" lang="c">    <span class="n" style="color: #333;">Vertices</span> <span class="n" style="color: #333;">m_vertices</span><span class="p">;</span></span>

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<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#cc89e9bae60f4855d94b92272217e92ebb5bcf52"><strong>Misc/samtobreak.hs</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">@@ -279,7 +279,7 @@ parseArgs = do</td>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="haskell">  <span class="kr" style="font-weight: 600;">where</span></span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="haskell">  <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">putStr</span> <span class="p">(</span><span class="n" style="color: #333;">usageInfo</span> <span class="n" style="color: #333;">usage</span> <span class="n" style="color: #333;">options</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">exitSuccess</span></span>

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<td class="diff-line-num new_line" data-linenumber="281" 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="LC281" class="line" lang="haskell">  <span class="n" style="color: #333;">tryHelp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Try 'abyss-samtobreak --help' for more information."</span></span>

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<td class="diff-line-num new_line old" data-linenumber="282" 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="LC282" class="line" lang="haskell">  <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"abyss-samtobreak (ABySS) 2.2.<span class="idiff left right">2</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="haskell">  <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"abyss-samtobreak (ABySS) 2.2.<span class="idiff left right">3</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="haskell">  <span class="n" style="color: #333;">usage</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Usage: samtobreak [OPTION]... [FILE]...</span><span class="se" style="color: #d14;">\n\</span></span>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="haskell"><span class="se" style="color: #d14;">\</span><span class="s" style="color: #d14;">Calculate contig and scaffold contiguity and correctness metrics.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="haskell"></span>

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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -330,8 +330,8 @@ verbose logging enabled:</td>

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="markdown">At the current time, the user must calculate suitable values for <span class="sb" style="color: #d14;">`B`</span> and <span class="sb" style="color: #d14;">`H`</span> on</span>

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="markdown">their own, and finding the best value for <span class="sb" style="color: #d14;">`kc`</span> may require experimentation</span>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="markdown">(optimal values are typically in the range of 2-4). Internally, the Bloom filter</span>

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<pre style="margin: 0;">-<span id="LC333" class="line" lang="markdown">assembler allocates the entire memory budget (<span class="sb" style="color: #d14;">`B`</span>) to a Counting Bloom filter,</span>

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="markdown">and an additional (<span class="sb" style="color: #d14;">`B/<span class="idiff left right">8</span>`</span>) memory to another Bloom filter that is used to track</span>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="markdown">assembler allocates the entire memory budget (<span class="sb" style="color: #d14;">`B<span class="idiff left right"> * 8/9</span>`</span>) to a Counting Bloom filter,</span>

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="markdown">and an additional (<span class="sb" style="color: #d14;">`B/<span class="idiff left right">9</span>`</span>) memory to another Bloom filter that is used to track</span>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="markdown">k-mers that have previously been included in contigs. Users are recommended to</span>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="markdown">target a Bloom filter false positive rate (FPR) that is less than 5%, as reported</span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="markdown">by the assembly log when using the <span class="sb" style="color: #d14;">`v=-v`</span> option (verbose level 1).</span>

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<li id="e9d1fc75e09569c2f720b16b5ad725181dd43d69">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#e9d1fc75e09569c2f720b16b5ad725181dd43d69"><strong>Unittest/BloomDBG/CountingBloomFilterTest.cpp</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">@@ -19,16 +19,17 @@ TEST(CountingBloomFilter, base) {</td>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"TGGACAGCGTTACCTC"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"TAATAACAGTCCCTAT"</span><span class="p">;</span></span>

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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">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"GATCGTGGCGGGCGAT"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"TTTTTTTTTTTTTTTT"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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

23

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

<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"></span>

</pre>

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

23

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

24

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp">  <span class="n" style="color: #333;">RollingHashIterator</span> <span class="n" style="color: #333;">itA</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">numHashes</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>

</pre>

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

24

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

25

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp">  <span class="n" style="color: #333;">RollingHashIterator</span> <span class="n" style="color: #333;">itB</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">numHashes</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>

</pre>

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

25

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

26

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp">  <span class="n" style="color: #333;">RollingHashIterator</span> <span class="n" style="color: #333;">itC</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">numHashes</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>

</pre>

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

26

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

27

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp">  <span class="n" style="color: #333;">RollingHashIterator</span> <span class="n" style="color: #333;">itD</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">numHashes</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" 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">

27

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<td class="diff-line-num new_line old" data-linenumber="28" 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="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hash</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>

</pre>

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

<td class="diff-line-num new old_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">

</td>

<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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<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="cpp">  <span class="n" style="color: #333;"><span class="idiff left">RollingHashIterator</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">itE</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">e</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numHashes</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">k</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" 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">

28

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

29

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

<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"></span>

</pre>

</td>

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

29

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

30

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

<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp">  <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">itA</span><span class="p">);</span></span>

</pre>

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

30

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<td class="diff-line-num new_line" data-linenumber="31" 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">

31

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

<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp">  <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">filtered_popcount</span><span class="p">(),</span> <span class="mi" style="color: #099;">0U</span><span class="p">);</span></span>

</pre>

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

<td class="diff-line-num old old_line" data-linenumber="31" 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">

31

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<td class="diff-line-num new_line old" data-linenumber="32" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp">  <span class="n" style="color: #333;">EXPECT_FALSE</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">contains</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="n" style="color: #333;"><span class="idiff right">hash</span></span><span class="p">));</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="32" 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="32" 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="LC32" class="line" lang="cpp">  <span class="n" style="color: #333;">EXPECT_FALSE</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">contains</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff right">itE</span></span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" 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">

32

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<td class="diff-line-num 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">

33

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

<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp">  <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">itA</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num 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">

33

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<td class="diff-line-num new_line" data-linenumber="34" 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">

34

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

<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp">  <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">filtered_popcount</span><span class="p">(),</span> <span class="mi" style="color: #099;">1U</span><span class="p">);</span></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="34" 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">

34

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

35

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

<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp">  <span class="n" style="color: #333;">EXPECT_TRUE</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">contains</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">itA</span><span class="p">));</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4"><strong>azure-pipelines.yml</strong></a>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="yaml">  <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="yaml">  <span class="pi">-</span> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="pi">|</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="yaml">      <span class="s" style="color: #d14;">brew update</span></span>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="yaml">      <span class="s" style="color: #d14;">brew install automake boost<span class="idiff left right">@1.70</span> openmpi google-sparsehash make pandoc ghc</span></span>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="yaml">      <span class="s" style="color: #d14;">brew install automake boost openmpi google-sparsehash make pandoc ghc</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install common</span></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="yaml">  <span class="pi">-</span> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="pi">|</span></span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="yaml">      <span class="s" style="color: #d14;">./autogen.sh</span></span>

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="yaml">      <span class="s" style="color: #d14;">./configure --with-boost=/usr/local/<span class="idiff left right">Cellar/boost/1.70.0/include/ --with-mpi=/usr/local/Cellar/open-mpi/4.0.1_2/ CPPFLAGS=-I/usr/local/Cellar/google-sparsehash/2.0.3/include/</span></span></span>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="yaml">      <span class="s" style="color: #d14;">./configure --with-boost=/usr/local/<span class="idiff left right">opt/boost/include --with-mpi=/usr/local/Cellar/open-mpi/4.0.1_2 CPPFLAGS=-I/usr/local/Cellar/google-sparsehash/2.0.3/include</span></span></span>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="yaml">      <span class="s" style="color: #d14;">make -j12 distcheck</span></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Compiling ABySS with default gcc</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="yaml"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="yaml"><span class="pi">-</span> <span class="na" style="color: #008080;">job</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux_gcc9</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="yaml">  <span class="na" style="color: #008080;">pool</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="yaml">    <span class="na" style="color: #008080;">vmImage</span><span class="pi">:</span> <span class="s" style="color: #d14;">Ubuntu </span><span class="m" style="color: #099;">16.04</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="yaml">  <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="yaml">  <span class="pi">-</span> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="yaml">      <span class="s" style="color: #d14;">sudo apt-get update -qq</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="169" 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">

169

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="yaml">      <span class="s" style="color: #d14;">sudo apt-get install -qq software-properties-common</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="170" 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">

170

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="yaml">      <span class="s" style="color: #d14;">sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="171" 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">

171

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="yaml">      <span class="s" style="color: #d14;">sudo apt-get update -qq</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="172" 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">

172

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="yaml">      <span class="s" style="color: #d14;">sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="173" 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">

173

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install common</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="174" 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">

174

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="yaml">  <span class="pi">-</span> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">sudo apt-get install -qq gcc-9 g++-9</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="175" 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">

175

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install gcc-9</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="176" 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">

176

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="yaml">  <span class="pi">-</span> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="177" 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">

177

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="yaml">      <span class="s" style="color: #d14;">./autogen.sh</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="178" 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">

178

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="yaml">      <span class="s" style="color: #d14;">export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-9 CXX=g++-9"</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="179" 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">

179

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="yaml">      <span class="s" style="color: #d14;">./configure CC=gcc-9 CXX=g++-9 --with-mpi=/usr/lib/openmpi</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="180" 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">

180

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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="LC180" class="line" lang="yaml">      <span class="s" style="color: #d14;">make -j12 distcheck</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="181" 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">

181

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Compiling ABySS with gcc-9</span></span></pre>

</td>

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</table>

<br>

</li>

<li id="cd06d399cbb97ac80091363ace10b558e194af5f">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#cd06d399cbb97ac80091363ace10b558e194af5f"><strong>bin/abyss-pe</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="398" 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="398" 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">@@ -398,7 +398,7 @@ help:</td>

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<td class="diff-line-num old_line" data-linenumber="398" 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">

398

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<td class="diff-line-num new_line" data-linenumber="398" 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">

398

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="plaintext">    @echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users@bcgsc.ca.'</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="399" 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">

399

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<td class="diff-line-num new_line" data-linenumber="399" 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">

399

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<pre style="margin: 0;"> <span id="LC399" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="400" 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">

400

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<td class="diff-line-num new_line" data-linenumber="400" 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">

400

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<pre style="margin: 0;"> <span id="LC400" class="line" lang="plaintext">version:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="401" 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">

401

</td>

<td class="diff-line-num new_line old" data-linenumber="401" 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="LC401" class="line" lang="plaintext">    @echo "abyss-pe (ABySS) 2.2.<span class="idiff left right">2</span>"</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="402" 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="401" 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">

401

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext">    @echo "abyss-pe (ABySS) 2.2.<span class="idiff left right">3</span>"</span>

</pre>

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</tr>

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<td class="diff-line-num old_line" data-linenumber="402" 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">

402

</td>

<td class="diff-line-num new_line" data-linenumber="402" 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">

402

</td>

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

<pre style="margin: 0;"> <span id="LC402" class="line" lang="plaintext">    @echo "Written by Shaun Jackman and Anthony Raymond."</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="403" 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">

403

</td>

<td class="diff-line-num new_line" data-linenumber="403" 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">

403

</td>

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

<pre style="margin: 0;"> <span id="LC403" class="line" lang="plaintext">    @echo</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="404" 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">

404

</td>

<td class="diff-line-num new_line" data-linenumber="404" 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">

404

</td>

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

<pre style="margin: 0;"> <span id="LC404" class="line" lang="plaintext">    @echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</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" id="" style="line-height: 1.6;">

<td class="diff-line-num old_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>

<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>

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

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">AC_PREREQ(2.62)</span>

</pre>

</td>

</tr>

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

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

2

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">AC_INIT(ABySS, 2.2.<span class="idiff left right">2</span>, abyss-users@bcgsc.ca, abyss,</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

</td>

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">AC_INIT(ABySS, 2.2.<span class="idiff left right">3</span>, abyss-users@bcgsc.ca, abyss,</span>

</pre>

</td>

</tr>

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

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

3

</td>

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

3

</td>

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">              http://www.bcgsc.ca/platform/bioinfo/software/abyss)</span>

</pre>

</td>

</tr>

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

<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

</td>

<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

</td>

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

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

</pre>

</td>

</tr>

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

<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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">AC_CONFIG_MACRO_DIR([m4])</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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 new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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">

</td>

<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">

1

</td>

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">abyss (2.2.3-1) unstable; urgency=medium</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</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

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<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">  * Remove strict-alignment patch as per upstream:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

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

5

</td>

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">    "Adding an additionally memcpy would slow down these inner-loop functions.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<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">     Architectures without hardware support for unaligned memory access are</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">     currently unsupported by ABySS."</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</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

</td>

<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">    https://github.com/bcgsc/abyss/pull/279#issuecomment-468079889</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<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

</td>

<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">  * Turn off the 32-bit patch for now. Local testing with i386 shows that it</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<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

</td>

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">    may not be needed as suggested by upstream.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sat, 28 Sep 2019 12:04:53 +0200</span>

</pre>

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13

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

</pre>

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1

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14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">abyss (2.2.2-1) unstable; urgency=medium</span>

</pre>

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2

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15

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

</pre>

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3

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">  * New upstream version</span>

</pre>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

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1

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1

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

</pre>

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2

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2

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

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">abyss-32-bit.patch</span>

</pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">strict_alignment.patch</span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">#abyss-32-bit.patch</span>

</pre>

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5

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4

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

</td>

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<br>

</li>

<li id="e4c19aed51618bf0c7ebd03189c67e422f84d4eb">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>

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1

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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 <michael.crusoe@gmail.com></span></span>

</pre>

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2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: typo fixes, courtesy lintian</span></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/bcgsc/abyss/pull/301</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- abyss.orig/Sealer/README.md</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ abyss/Sealer/README.md</span></span>

</pre>

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -24,7 +24,7 @@</span></span>

</pre>

</td>

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<br>

</li>

<li id="6091197197b5b3ed653a0d23955ce03d57fb83d3">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#6091197197b5b3ed653a0d23955ce03d57fb83d3"><strong>debian/patches/strict_alignment.patch</strong>

deleted

</a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC1" class="line" lang="diff"><span class="p">Author: David Matthew Mattli <dmm@mattli.us></span></span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Change: Fri, 2 Feb 2018 15:28:32 +0000 (by James Clarke <jrtc27@debian.org>)</span></span>

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/889147</span></span>

</pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: https://github.com/bcgsc/abyss/pull/279</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC5" class="line" lang="diff"><span class="p">Description: Fix strict alignment violation on sparc64</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" 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">

6

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC6" class="line" lang="diff"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="7" 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">

7

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC7" class="line" lang="diff">--- a/Common/Kmer.cpp</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

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Common/Kmer.cpp</span></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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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -188,7 +188,8 @@</span> static Seq load(const uint8_t *src)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" 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">

10

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC10" class="line" lang="diff">  Seq seq;</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="11" 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">

11

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC11" class="line" lang="diff"> #if MAX_KMER > 96</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" 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">

12

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC12" class="line" lang="diff"> # if WORDS_BIGENDIAN</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13" 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">

13

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const size_t *s = reinterpret_cast<const size_t*>(src);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" 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">

14

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ size_t s[Kmer::NUM_BYTES / sizeof(size_t)];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" 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">

15

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ memcpy(s, src, Kmer::NUM_BYTES);</span></span>

</pre>

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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">

16

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<td class="diff-line-num new_line old" data-linenumber="0" 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="diff">  size_t *d = reinterpret_cast<size_t*>(&seq + 1);</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">

17

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<td class="diff-line-num new_line old" data-linenumber="0" 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="diff">  copy(s, s + Kmer::NUM_BYTES/sizeof(size_t), reverse_iterator<size_t*>(d));</span>

</pre>

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

18

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC18" class="line" lang="diff"> # else</span>

</pre>

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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">

19

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<td class="diff-line-num new_line old" data-linenumber="0" 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="diff"><span class="p">@@ -235,9 +236,10 @@</span> static void storeReverse(uint8_t *dest,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" 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="0" 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="LC20" class="line" lang="diff"> #if MAX_KMER > 96</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" 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">

21

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC21" class="line" lang="diff"> # if WORDS_BIGENDIAN</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" 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="0" 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="LC22" class="line" lang="diff">  const size_t *s = reinterpret_cast<const size_t*>(&seq);</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" 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="0" 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="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- size_t *d = reinterpret_cast<size_t*>(dest);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" 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">

24

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ size_t d[Kmer::NUM_BYTES / sizeof(size_t)];</span></span>

</pre>

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25

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff">  copy(s, s + Kmer::NUM_BYTES/sizeof(size_t),</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="26" 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">

26

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff">                  reverse_iterator<size_t*>(d +  Kmer::NUM_BYTES/sizeof(size_t)));</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="27" 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">

27

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ memcpy(dest, d, Kmer::NUM_BYTES);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="28" 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">

28

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff">  reverse(dest, dest + Kmer::NUM_BYTES);</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="29" 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">

29

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> # else</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="30" 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">

30

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff">  memcpy(dest, &seq, Kmer::NUM_BYTES);</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#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" id="" style="line-height: 1.6;">

<td class="diff-line-num old_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>

<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>

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

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</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

</td>

<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

</td>

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

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

</pre>

</td>

</tr>

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

<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

</td>

<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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">export DEB_CXXFLAGS_MAINT_APPEND = -DGTEST_USE_OWN_TR1_TUPLE=0<span class="idiff left right"> -Wno-error=deprecated-copy -Wno-error=array-bounds</span></span>

</pre>

</td>

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

<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

</td>

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">export DEB_CXXFLAGS_MAINT_APPEND = -DGTEST_USE_OWN_TR1_TUPLE=0</span>

</pre>

</td>

</tr>

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

<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

</td>

<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

</td>

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

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

</pre>

</td>

</tr>

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

<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

</td>

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</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="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

</td>

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

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

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="54545de904c655f7c6b1ed6e0f6e947540dbf202">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#54545de904c655f7c6b1ed6e0f6e947540dbf202"><strong>doc/ABYSS.1</strong></a>

<hr>

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

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

1

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.2.<span class="idiff left right">2</span>" "User Commands"</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

1

</td>

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.2.<span class="idiff left right">3</span>" "User Commands"</span>

</pre>

</td>

</tr>

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

<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

</td>

<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

</td>

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

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

</pre>

</td>

</tr>

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

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

3

</td>

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

3

</td>

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">ABYSS \- assemble short reads into contigs</span>

</pre>

</td>

</tr>

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

<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

</td>

<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

</td>

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

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

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="210a6761e540ac8179e4a92fdffba66759a77e27">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#210a6761e540ac8179e4a92fdffba66759a77e27"><strong>doc/abyss-pe.1</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 old" id="" style="line-height: 1.6;">

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

1

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.<span class="idiff left right">2</span>" "User Commands"</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

1

</td>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.<span class="idiff left right">3</span>" "User Commands"</span>

</pre>

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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">.SH NAME</span>

</pre>

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

3

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

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">abyss-pe - assemble reads into contigs</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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

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

</pre>

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</table>

<br>

</li>

<li id="58b9c1ec4a434e1b73496c894a35770e972461a5">

<a href="https://salsa.debian.org/med-team/abyss/compare/c7f5402a4a10b145c64d73e3e8f15c65247dc62a...a3f928f99577bb66c920920def6528fb74faf572#58b9c1ec4a434e1b73496c894a35770e972461a5"><strong>doc/abyss-tofastq.1</strong></a>

<hr>

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

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

1

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<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="plaintext">.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.<span class="idiff left right">2</span>" "User Commands"</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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">

1

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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="LC1" class="line" lang="plaintext">.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.<span class="idiff left right">3</span>" "User Commands"</span>

</pre>

</td>

</tr>

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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

</td>

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

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

</pre>

</td>

</tr>

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

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

3

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

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">abyss-tofastq \- convert various file formats to FASTQ format</span>

</pre>

</td>

</tr>

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

<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

</td>

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

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

</pre>

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