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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/abyss">Debian Med / abyss</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/abyss/commit/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>
<li>
<strong><a href="https://salsa.debian.org/med-team/abyss/commit/0a1fc576efe1d1e1306199a3d2d129c266e9da4d">0a1fc576</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-08-17T06:53:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.2.2'
Update to upstream version '2.2.2'
with Debian dir d6b938f5772465a8fcf0713e7e5fec7a945c4c33</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/abyss/commit/8ae4d4269da3fed6f4af2feedab7b91850bf5b6d">8ae4d426</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-08-17T06:53:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/abyss/commit/74298696a060ea9876f79a8d32af9aada7ece73c">74298696</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-08-17T07:23:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">spelling fixes + Upload to unstable
</pre>
</li>
</ul>
<h4>17 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="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#f5f51601866c86e59a004bd93fa415f5675be8c5">
<span class="new-file">
+
debian/clean
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<span class="new-file">
+
debian/patches/spelling
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#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/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c#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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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">checkout</span></span>
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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>
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC24" class="line" lang="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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>
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<td class="diff-line-num 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">
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC37" class="line" lang="yaml"> <span class="no" style="color: #008080;">./autogen.sh</span></span>
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<td class="diff-line-num new old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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>
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<td class="diff-line-num old_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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<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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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(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="40" style="width: 35px; color: rgba(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="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>
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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>
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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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<td class="diff-line-num 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">
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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>
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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(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="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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<pre style="margin: 0;"> <span id="LC55" class="line" lang="yaml"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -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>
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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>
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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>
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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>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="yaml"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -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>
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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>
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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>
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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>
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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>
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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>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2019-08-16 Johnathan Wong <jowong@bcgsc.ca></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Release version 2.2.2</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Fix abyss-overlap for 32-bit systems</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * Release version 2.2.1</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -146,7 +146,7 @@ static void buildFMIndex(FMIndex& fm, const string& path)</td>
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146
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146
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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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147
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147
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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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148
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"></span>
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149
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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>
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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>
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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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151
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151
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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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152
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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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<a href="https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c#197f3c03e87c699170a7ecc6d82eeef3501327a0"><strong>Map/map.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -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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506
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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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<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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<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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<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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510
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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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511
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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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<a href="https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c#972410a34e360bcb40259fc062cf285017dc5b50"><strong>Map/overlap.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -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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294
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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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295
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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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<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>
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<a href="https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c#cc89e9bae60f4855d94b92272217e92ebb5bcf52"><strong>Misc/samtobreak.hs</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -279,7 +279,7 @@ parseArgs = do</td>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="haskell"> <span class="kr" style="font-weight: 600;">where</span></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="haskell"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">putStr</span> <span class="p">(</span><span class="n" style="color: #333;">usageInfo</span> <span class="n" style="color: #333;">usage</span> <span class="n" style="color: #333;">options</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">exitSuccess</span></span>
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281
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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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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="haskell"> <span class="n" style="color: #333;">usage</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Usage: samtobreak [OPTION]... [FILE]...</span><span class="se" style="color: #d14;">\n\</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="haskell"><span class="se" style="color: #d14;">\</span><span class="s" style="color: #d14;">Calculate contig and scaffold contiguity and correctness metrics.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="haskell"></span>
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<a href="https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c#40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4"><strong>azure-pipelines.yml</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -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>
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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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<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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,6 +36,7 @@ jobs:</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>
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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>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,6 +56,7 @@ jobs:</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>
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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>
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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>
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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>
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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>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -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>
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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>
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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>
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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>
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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>
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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>
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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="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>
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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>
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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>
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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>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -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>
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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>
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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>
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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>
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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>
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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>
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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>
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<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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<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>
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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>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="yaml"></span>
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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>
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149
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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>
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144
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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>
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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>
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146
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<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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154
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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>
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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>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="yaml"> <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install common</span></span>
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<pre style="margin: 0;">-<span id="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>
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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>
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153
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="yaml"> <span class="no" style="color: #008080;">./autogen.sh</span></span>
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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>
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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>
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156
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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>
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157
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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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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="yaml"> <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Compiling ABySS with <span class="idiff left right">default gcc</span></span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -398,7 +398,7 @@ help:</td>
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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>
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399
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="plaintext">version:</span>
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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">1</span>"</span>
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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>
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="plaintext"> @echo "Written by Shaun Jackman and Anthony Raymond."</span>
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="plaintext"> @echo</span>
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404
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404
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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>
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<a href="https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">AC_PREREQ(2.62)</span>
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2
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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>
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2
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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">2</span>, abyss-users@bcgsc.ca, abyss,</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> http://www.bcgsc.ca/platform/bioinfo/software/abyss)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">AC_CONFIG_MACRO_DIR([m4])</span>
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<a href="https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">abyss (2.2.2-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Sat, 17 Aug 2019 08:53:07 +0200</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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1
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">abyss (2.2.1-1) unstable; urgency=medium</span>
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2
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream release, should fix failing builds on 32-bit architectures.</span>
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<a href="https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c#f5f51601866c86e59a004bd93fa415f5675be8c5"><strong>debian/clean</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Sealer/abyss-sealer.1</span></pre>
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<a href="https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,3 +2,4 @@ abyss-pe.patch</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"># gtest.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">abyss-32-bit.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">strict_alignment.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">spelling</span></pre>
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<a href="https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: typo fixes, courtesy lintian</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- abyss.orig/Sealer/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ abyss/Sealer/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -24,7 +24,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> Description</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> ===========</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Sealer is an application of Konnector that closes intra-scaffold gaps. It performs three sequential functions. First, regions with Ns are identified from an input scaffold. Flanking nucleotues (2 x 100bp) are extracted from those regions while respecting the strand (5' to 3') direction on the sequence immediately downstream of each gap. In the second step, flanking sequence pairs are used as input to Konnector along with a set of reads with a high level of coverage redundancy. Ideally, the reads should represent the original dataset from which the draft assembly is generated, or further whole genome shotgun (WGS) sequencing data generated from the same sample. Within Konnector, the input WGS reads are used to populate a Bloom filter, tiling the reads with a sliding window of length *k*, thus generating a probabilistic representation of all the *k*-mers in the reads. Konnector also uses crude error removal and correctional algorithms, eliminating singletons (*k*-mers that are observed only once) and fixing base mismatches in the flanking sequence pairs. Sealer launches Konnector processes using a user-input range of *k*-mer lengths. In the third and final operation, succesfully merged sequences are inserted into the gaps of the original scaffolds, and Sealer outputs a new gap-filled scaffold file.</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Sealer is an application of Konnector that closes intra-scaffold gaps. It performs three sequential functions. First, regions with Ns are identified from an input scaffold. Flanking nucleotues (2 x 100bp) are extracted from those regions while respecting the strand (5' to 3') direction on the sequence immediately downstream of each gap. In the second step, flanking sequence pairs are used as input to Konnector along with a set of reads with a high level of coverage redundancy. Ideally, the reads should represent the original dataset from which the draft assembly is generated, or further whole genome shotgun (WGS) sequencing data generated from the same sample. Within Konnector, the input WGS reads are used to populate a Bloom filter, tiling the reads with a sliding window of length *k*, thus generating a probabilistic representation of all the *k*-mers in the reads. Konnector also uses crude error removal and correctional algorithms, eliminating singletons (*k*-mers that are observed only once) and fixing base mismatches in the flanking sequence pairs. Sealer launches Konnector processes using a user-input range of *k*-mer lengths. In the third and final operation, successfully merged sequences are inserted into the gaps of the original scaffolds, and Sealer outputs a new gap-filled scaffold file.</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> Installation</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> ============</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -159,6 +159,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> * `--help`: display this help and exit</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> * `--version`: output version information and exit</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-*k* is the size of *k*-mer for the de Bruijn graph. You may specify multiple values of *k*, which will increase the nubmer of gaps closed at the cost of increased run time. Multiple values of *k* ought to be specified in increasing order, as lower values of *k* have fewer coverage gaps and are less likely to misassemble.</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+*k* is the size of *k*-mer for the de Bruijn graph. You may specify multiple values of *k*, which will increase the number of gaps closed at the cost of increased run time. Multiple values of *k* ought to be specified in increasing order, as lower values of *k* have fewer coverage gaps and are less likely to misassemble.</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> *P* is the threshold for number of paths allowed to be traversed. When set to 10, Konnector will attempt to close gaps even when there are 10 different paths found. It would attempt to create a consensus sequence between these paths. The default setting is 2.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- abyss.orig/doc/abyss-pe.1</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ abyss/doc/abyss-pe.1</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -113,7 +113,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> SS=--SS to assemble in strand-specific mode</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> .br</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> Requires that all libraries are strand-specific RNA-Seq libraries.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Assumes that the first read in a read pair is reveresed WRT the</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Assumes that the first read in a read pair is reversed WRT the</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> transcripts sequenced.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> .TP</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> .B t</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">@@ -242,7 +242,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> .SS "MPI COMPATIBILITY"</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> Due to its use of multi-threading, DIDA has known deadlocking issues</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-with OpenMPI. Using the MPICH MPI library is strongly recommmended</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+with OpenMPI. Using the MPICH MPI library is strongly recommended</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> when running assemblies with DIDA. Testing was done with MPICH 3.1.3,</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> compiled with --enable-threads=funneled.</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">export DEB_CXXFLAGS_MAINT_APPEND = -DGTEST_USE_OWN_TR1_TUPLE=0</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">export DEB_CXXFLAGS_MAINT_APPEND = -DGTEST_USE_OWN_TR1_TUPLE=0<span class="idiff left right"> -Wno-error=deprecated-copy -Wno-error=array-bounds</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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<a href="https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c#54545de904c655f7c6b1ed6e0f6e947540dbf202"><strong>doc/ABYSS.1</strong></a>
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<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>
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<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>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">ABYSS \- assemble short reads into contigs</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<a href="https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c#210a6761e540ac8179e4a92fdffba66759a77e27"><strong>doc/abyss-pe.1</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.<span class="idiff left right">1</span>" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.<span class="idiff left right">2</span>" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">abyss-pe - assemble reads into contigs</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<a href="https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c#58b9c1ec4a434e1b73496c894a35770e972461a5"><strong>doc/abyss-tofastq.1</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.<span class="idiff left right">1</span>" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.<span class="idiff left right">2</span>" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">abyss-tofastq \- convert various file formats to FASTQ format</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">.br</span>
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