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GitLab

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<h3>

Michael R. Crusoe pushed to branch upstream

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/6ab3b0995a34b1a177a00f5d944c326400a0b576">6ab3b099</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-08-17T06:53:02Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.2.2</pre>

</li>

</ul>

<h4>12 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#fd5da61396a8376845bee5cdf71aaf3c98a888ae">

.circleci/config.yml

</a>

</li>

<li class="file-stats">

<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">

ChangeLog

</a>

</li>

<li class="file-stats">

<a href="#42dfa7ac34a62a2187885067de9ebaa9cd1fa49e">

Map/index.cc

</a>

</li>

<li class="file-stats">

<a href="#197f3c03e87c699170a7ecc6d82eeef3501327a0">

Map/map.cc

</a>

</li>

<li class="file-stats">

<a href="#972410a34e360bcb40259fc062cf285017dc5b50">

Map/overlap.cc

</a>

</li>

<li class="file-stats">

<a href="#cc89e9bae60f4855d94b92272217e92ebb5bcf52">

Misc/samtobreak.hs

</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="#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="fd5da61396a8376845bee5cdf71aaf3c98a888ae">

<a href="https://salsa.debian.org/med-team/abyss/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576#fd5da61396a8376845bee5cdf71aaf3c98a888ae"><strong>.circleci/config.yml</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +21,7 @@ jobs:</td>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml">      <span class="pi">-</span> <span class="s" style="color: #d14;">checkout</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">

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

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></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">

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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">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml">          <span class="no" style="color: #008080;">./autogen.sh</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml">          <span class="no" style="color: #008080;">export DISTCHECK_CONFIGURE_FLAGS="CC=clang-6.0 CXX=clang++-6.0"</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">

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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">

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

<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml">          <span class="no" style="color: #008080;">./configure CC=clang-6.0 CXX=clang++-6.0 --with-mpi=/usr/lib/openmpi</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">

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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">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">make -j12 distcheck</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">

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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">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml"></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,6 +35,7 @@ jobs:</td>

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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="yaml">      <span class="pi">-</span> <span class="s" style="color: #d14;">checkout</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="36" 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="LC36" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="yaml">          <span class="no" style="color: #008080;">./autogen.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml">          <span class="no" style="color: #008080;">export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-5 CXX=g++-5"</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="39" 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="LC39" class="line" lang="yaml">          <span class="no" style="color: #008080;">./configure CC=gcc-5 CXX=g++-5 --with-mpi=/usr/lib/openmpi</span></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">make -j12 distcheck</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="41" 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="LC41" class="line" lang="yaml"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="47" 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="49" 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">@@ -47,6 +49,7 @@ jobs:</td>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="yaml">      <span class="pi">-</span> <span class="s" style="color: #d14;">checkout</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="yaml">          <span class="no" style="color: #008080;">./autogen.sh</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml">          <span class="no" style="color: #008080;">export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-6 CXX=g++-6"</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="yaml">          <span class="no" style="color: #008080;">./configure CC=gcc-6 CXX=g++-6 --with-mpi=/usr/lib/openmpi</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">make -j12 distcheck</span></span>

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<td class="diff-line-num old_line" data-linenumber="52" 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="LC55" class="line" lang="yaml"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" 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="63" 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">@@ -60,6 +63,7 @@ jobs:</td>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="yaml">      <span class="pi">-</span> <span class="s" style="color: #d14;">checkout</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="yaml">          <span class="no" style="color: #008080;">./autogen.sh</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml">          <span class="no" style="color: #008080;">export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-7 CXX=g++-7"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="yaml">          <span class="no" style="color: #008080;">./configure CC=gcc-7 CXX=g++-7 --with-mpi=/usr/lib/openmpi</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">make -j12 distcheck</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="yaml"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" 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="77" 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">@@ -73,6 +77,7 @@ jobs:</td>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="yaml">      <span class="pi">-</span> <span class="s" style="color: #d14;">checkout</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="yaml">          <span class="no" style="color: #008080;">./autogen.sh</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="yaml">          <span class="no" style="color: #008080;">export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-8 CXX=g++-8"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="yaml">          <span class="no" style="color: #008080;">./configure CC=gcc-8 CXX=g++-8 --with-mpi=/usr/lib/openmpi</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">make -j12 distcheck</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="yaml"></span>

</pre>

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</li>

<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">

<a href="https://salsa.debian.org/med-team/abyss/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>

<hr>

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<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">

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

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2019-08-16  Johnathan Wong <jowong@bcgsc.ca></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">      * Release version 2.2.2</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">      * Fix abyss-overlap for 32-bit systems</span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">2019-08-12  Johnathan Wong <jowong@bcgsc.ca></span>

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

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3

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

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">      * Release version 2.2.1</span>

</pre>

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<br>

</li>

<li id="42dfa7ac34a62a2187885067de9ebaa9cd1fa49e">

<a href="https://salsa.debian.org/med-team/abyss/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576#42dfa7ac34a62a2187885067de9ebaa9cd1fa49e"><strong>Map/index.cc</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="146" 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="146" 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">@@ -146,7 +146,7 @@ static void buildFMIndex(FMIndex& fm, const string& path)</td>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FMIndex</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value_type</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp">  <span class="n" style="color: #333;">readFile</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"></span>

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<td class="diff-line-num old old_line" data-linenumber="149" 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="149" 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="LC149" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">size</span>_t</span> <span class="n" style="color: #333;">MAX_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FMIndex</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sais_size_type</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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="LC149" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint64</span>_t</span> <span class="n" style="color: #333;">MAX_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FMIndex</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sais_size_type</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</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;">MAX_SIZE</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="151" 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="LC151" class="line" lang="cpp">          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">PROGRAM</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">": `"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"', "</span></span>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp">                  <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">toSI</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span></span>

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<li id="197f3c03e87c699170a7ecc6d82eeef3501327a0">

<a href="https://salsa.debian.org/med-team/abyss/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576#197f3c03e87c699170a7ecc6d82eeef3501327a0"><strong>Map/map.cc</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="505" 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="505" 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">@@ -505,7 +505,7 @@ static void buildFMIndex(FMIndex& fm, const char* path)</td>

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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FMIndex</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value_type</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp">  <span class="n" style="color: #333;">readFile</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC507" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line old" data-linenumber="508" 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="LC508" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">size</span>_t</span> <span class="n" style="color: #333;">MAX_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FMIndex</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sais_size_type</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>

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<td class="diff-line-num new old_line" data-linenumber="509" 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="LC508" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint64</span>_t</span> <span class="n" style="color: #333;">MAX_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FMIndex</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sais_size_type</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>

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<td class="diff-line-num new_line" data-linenumber="509" 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="LC509" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</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;">MAX_SIZE</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="510" 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">

510

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<td class="diff-line-num new_line" data-linenumber="510" 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="LC510" class="line" lang="cpp">          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">PROGRAM</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">": `"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"', "</span></span>

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<td class="diff-line-num new_line" data-linenumber="511" 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="LC511" class="line" lang="cpp">                  <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">toSI</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span></span>

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<li id="972410a34e360bcb40259fc062cf285017dc5b50">

<a href="https://salsa.debian.org/med-team/abyss/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576#972410a34e360bcb40259fc062cf285017dc5b50"><strong>Map/overlap.cc</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="293" 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="293" 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">@@ -293,7 +293,7 @@ static void buildFMIndex(FMIndex& fm, const char* path)</td>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FMIndex</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value_type</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp">  <span class="n" style="color: #333;">readFile</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">size</span>_t</span> <span class="n" style="color: #333;">MAX_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FMIndex</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sais_size_type</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>

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<td class="diff-line-num new old_line" data-linenumber="297" 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="LC296" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint64</span>_t</span> <span class="n" style="color: #333;">MAX_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FMIndex</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sais_size_type</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</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;">MAX_SIZE</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp">          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">PROGRAM</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">": `"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"', "</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp">                  <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">toSI</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span></span>

</pre>

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<li id="cc89e9bae60f4855d94b92272217e92ebb5bcf52">

<a href="https://salsa.debian.org/med-team/abyss/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576#cc89e9bae60f4855d94b92272217e92ebb5bcf52"><strong>Misc/samtobreak.hs</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="279" 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="279" 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">@@ -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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<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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<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">1</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">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="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>

</pre>

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</li>

<li id="40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4">

<a href="https://salsa.debian.org/med-team/abyss/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576#40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4"><strong>azure-pipelines.yml</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,6 +16,7 @@ jobs:</td>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install 32-bit compilation support</span></span>

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<pre style="margin: 0;"> <span id="LC17" 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="LC18" class="line" lang="yaml">      <span class="no" style="color: #008080;">./autogen.sh</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml">      <span class="no" style="color: #008080;">export DISTCHECK_CONFIGURE_FLAGS="CC=\"gcc-8 -m32\" CXX=\"g++-8 -m32\" --build=i386-linux-gnu"</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml">      <span class="no" style="color: #008080;">./configure CC=gcc-8 CXX=g++-8 --build=i686-linux-gnu "CFLAGS=-m32" "CXXFLAGS=-m32" "LDFLAGS=-m32" --with-mpi=/usr/lib/openmpi</span></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml">      <span class="no" style="color: #008080;">make -j12 distcheck</span></span>

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

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<pre style="margin: 0;"> <span id="LC22" 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-8</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install clang-6.0</span></span>

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<pre style="margin: 0;"> <span id="LC37" 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="LC38" class="line" lang="yaml">      <span class="no" style="color: #008080;">./autogen.sh</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml">      <span class="no" style="color: #008080;">export DISTCHECK_CONFIGURE_FLAGS="CC=clang-6.0 CXX=clang++-6.0"</span></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="yaml">      <span class="no" style="color: #008080;">./configure CC=clang-6.0 CXX=clang++-6.0 --with-mpi=/usr/lib/openmpi</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="yaml">      <span class="no" style="color: #008080;">make -j12 distcheck</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="42" 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="LC42" 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 clang 6.0</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" 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="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install gcc-5</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC57" 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="LC58" class="line" lang="yaml">      <span class="no" style="color: #008080;">./autogen.sh</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="yaml">      <span class="no" style="color: #008080;">export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-5 CXX=g++-5"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="yaml">      <span class="no" style="color: #008080;">./configure CC=gcc-5 CXX=g++-5 --with-mpi=/usr/lib/openmpi</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="yaml">      <span class="no" style="color: #008080;">make -j12 distcheck</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="62" 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="LC62" 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-5</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" 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="76" 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">@@ -73,6 +76,7 @@ jobs:</td>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install gcc-6</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC77" 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="LC78" class="line" lang="yaml">      <span class="no" style="color: #008080;">./autogen.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="79" 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="LC79" class="line" lang="yaml">      <span class="no" style="color: #008080;">export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-6 CXX=g++-6"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="yaml">      <span class="no" style="color: #008080;">./configure CC=gcc-6 CXX=g++-6 --with-mpi=/usr/lib/openmpi</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="yaml">      <span class="no" style="color: #008080;">make -j12 distcheck</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC82" 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-6</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" 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="96" 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">@@ -92,6 +96,7 @@ jobs:</td>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install gcc-7</span></span>

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<pre style="margin: 0;"> <span id="LC97" 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="LC98" class="line" lang="yaml">      <span class="no" style="color: #008080;">./autogen.sh</span></span>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="yaml">      <span class="no" style="color: #008080;">export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-7 CXX=g++-7"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="yaml">      <span class="no" style="color: #008080;">./configure CC=gcc-7 CXX=g++-7 --with-mpi=/usr/lib/openmpi</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="yaml">      <span class="no" style="color: #008080;">make -j12 distcheck</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="102" 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="LC102" 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-7</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" 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="116" 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">@@ -111,6 +116,7 @@ jobs:</td>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install gcc-8</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC117" 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 old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="118" 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="LC118" class="line" lang="yaml">      <span class="no" style="color: #008080;">./autogen.sh</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" 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="119" 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="LC119" class="line" lang="yaml">      <span class="no" style="color: #008080;">export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-8 CXX=g++-8"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="120" 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="LC120" class="line" lang="yaml">      <span class="no" style="color: #008080;">./configure CC=gcc-8 CXX=g++-8 --with-mpi=/usr/lib/openmpi</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="121" 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="LC121" class="line" lang="yaml">      <span class="no" style="color: #008080;">make -j12 distcheck</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC122" 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-8</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" 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="146" 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">@@ -140,7 +146,7 @@ jobs:</td>

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<td class="diff-line-num old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="146" 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="LC146" 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;">make clang-format</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="147" 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="LC147" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Run clang-format</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="148" 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="LC148" class="line" lang="yaml"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="143" 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="149" 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="LC143" 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;">macOS_<span class="idiff left right">gcc8</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="144" 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="149" 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="LC149" 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;">macOS_<span class="idiff left right">default_gcc</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="150" 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="LC150" class="line" lang="yaml">  <span class="na" style="color: #008080;">pool</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="151" 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="LC151" class="line" lang="yaml">    <span class="na" style="color: #008080;">vmImage</span><span class="pi">:</span> <span class="s" style="color: #d14;">macOS-10.14</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="152" 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="LC152" class="line" lang="yaml">  <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" 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="154" 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">@@ -148,10 +154,8 @@ jobs:</td>

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<td class="diff-line-num old_line" data-linenumber="148" 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="LC154" class="line" lang="yaml">      <span class="no" style="color: #008080;">brew update</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="155" 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="LC155" class="line" lang="yaml">      <span class="no" style="color: #008080;">brew install automake boost@1.70 openmpi google-sparsehash make pandoc ghc</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="156" 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="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="151" 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="157" 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="LC151" 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;">brew install gcc@8</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="152" 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="157" 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="LC152" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install gcc</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="153" 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="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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="158" 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="LC158" class="line" lang="yaml">      <span class="no" style="color: #008080;">./autogen.sh</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="155" 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="159" 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="LC155" class="line" lang="yaml">      <span class="no" style="color: #008080;">./configure <span class="idiff left right">CC=gcc-8 CXX=g++-8 </span>--with-boost=/usr/local/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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" 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="159" 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="LC159" class="line" lang="yaml">      <span class="no" style="color: #008080;">./configure --with-boost=/usr/local/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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="156" 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">

156

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<td class="diff-line-num new_line" data-linenumber="160" 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">

160

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="yaml">      <span class="no" style="color: #008080;">make -j12 distcheck</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="157" 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">

157

</td>

<td class="diff-line-num new_line old" data-linenumber="161" 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>

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<pre style="margin: 0;">-<span id="LC157" 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 <span class="idiff left right">gcc 8</span></span></span></pre>

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<td class="diff-line-num new old_line" data-linenumber="158" 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="161" 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">

161

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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="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 <span class="idiff left right">default gcc</span></span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="cd06d399cbb97ac80091363ace10b558e194af5f">

<a href="https://salsa.debian.org/med-team/abyss/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576#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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<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>

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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

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<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">1</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">2</span>"</span>

</pre>

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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>

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<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

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<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>

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<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>

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<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/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576#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>

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<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">

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">AC_INIT(ABySS, 2.2.<span class="idiff left right">1</span>, abyss-users@bcgsc.ca, abyss,</span>

</pre>

</td>

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<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

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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="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>

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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

</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>

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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

</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>

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

5

</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="54545de904c655f7c6b1ed6e0f6e947540dbf202">

<a href="https://salsa.debian.org/med-team/abyss/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576#54545de904c655f7c6b1ed6e0f6e947540dbf202"><strong>doc/ABYSS.1</strong></a>

<hr>

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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">1</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">

</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">2</span>" "User Commands"</span>

</pre>

</td>

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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">.SH NAME</span>

</pre>

</td>

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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

</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>

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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

</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/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576#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">

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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-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.<span class="idiff left right">1</span>" "User Commands"</span>

</pre>

</td>

</tr>

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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">

</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-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" 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-pe - assemble 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="58b9c1ec4a434e1b73496c894a35770e972461a5">

<a href="https://salsa.debian.org/med-team/abyss/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576#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

</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-tofastq "1" "2015-May" "ABySS 2.2.<span class="idiff left right">1</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-tofastq "1" "2015-May" "ABySS 2.2.<span class="idiff left right">2</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-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

</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">.br</span>

</pre>

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