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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/minia">Debian Med / minia</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/-/commit/8313b9f2a5c7854124790300dc75b9bf7254ca44">8313b9f2</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-08-10T19:16:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/-/commit/aa02a815877b912193a9afff90b813ca11003667">aa02a815</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-08-10T19:16:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2.1+git20200607.bfd91a7</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/-/commit/0253a5697256ded88a470689115cb26d05f08bcb">0253a569</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-08-10T19:16:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.2.1+git20200607.bfd91a7'
Update to upstream version '3.2.1+git20200607.bfd91a7'
with Debian dir ba650caee2b6ea02ae84f30eea95311aae11edaa</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/-/commit/69be593ae0947f11a4d59c8cac74675de9da27d1">69be593a</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-08-10T19:16:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/-/commit/4392d647da351a535328a253fb21ce54da2d9746">4392d647</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-08-10T19:21:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Moving back to the release track.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/-/commit/82ffc645face3f630075fb00d3b7dee8ffd2b825">82ffc645</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-08-10T19:22:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2.4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/-/commit/547b1bcf225c6b1bd46389b264c415ca82eacefe">547b1bcf</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-08-10T19:22:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.2.4'
Update to upstream version '3.2.4'
with Debian dir f3ca7f6999c3455eaba2c7a0694915f785e75a6b</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#d30efc9627d8c8f9e646d5bcb3bb6c9fe6b8301d">
src/Minia.cpp
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/minia/-/compare/b74c92b79e6fb0cd0af64baaf4c550d1fd0ad722...547b1bcf225c6b1bd46389b264c415ca82eacefe#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ cmake_minimum_required (VERSION 2.6)</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># The default version number is the latest official build</span></span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_MAJOR 3<span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_MINOR 2<span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_PATCH <span class="idiff left right">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_PATCH <span class="idiff left right">4</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cmake"></span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># But, it is possible to define another release number during a local build</span></span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">IF</span> <span class="p">(</span>DEFINED MAJOR<span class="p">)</span></span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/minia/-/compare/b74c92b79e6fb0cd0af64baaf4c550d1fd0ad722...547b1bcf225c6b1bd46389b264c415ca82eacefe#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">minia (3.2.4-1) 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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * d/watch - using regular releases again (up from 3.2.1 to 3.2.4)</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"> -- Steffen Moeller <moeller@debian.org> Mon, 10 Aug 2020 19:16:26 +0200</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">minia (3.2.1+git20200522.4960a99-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/minia/-/compare/b74c92b79e6fb0cd0af64baaf4c550d1fd0ad722...547b1bcf225c6b1bd46389b264c415ca82eacefe#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -4,7 +4,7 @@ Uploaders: Olivier Sallou <osallou@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> bc,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> zlib1g-dev,</span>
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<a href="https://salsa.debian.org/med-team/minia/-/compare/b74c92b79e6fb0cd0af64baaf4c550d1fd0ad722...547b1bcf225c6b1bd46389b264c415ca82eacefe#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</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">opts="mode=git,pretty=3.2.1+git%cd.%h" \</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> https://github.com/GATB/minia.git HEAD</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">https://github.com/GATB/minia/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</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="LC6" class="line" lang="plaintext"># Released version is not compatible with gatb-core 1.4.1+git20191130.664696c+dfsg</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># So stick to latest Git commit for the moment</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># https://github.com/GATB/minia/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"># Once upon a time, the released version was not compatible with gatb-core 1.4.1+git20191130.664696c+dfsg</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"># That is we sticked to latest Git commit back then.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">#opts="mode=git,pretty=3.2.1+git%cd.%h" \</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"># https://github.com/GATB/minia.git HEAD</span></pre>
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<a href="https://salsa.debian.org/med-team/minia/-/compare/b74c92b79e6fb0cd0af64baaf4c550d1fd0ad722...547b1bcf225c6b1bd46389b264c415ca82eacefe#d30efc9627d8c8f9e646d5bcb3bb6c9fe6b8301d"><strong>src/Minia.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -250,7 +250,7 @@ string Minia::assemble (/*const, removed because Simplifications isn't const any</td>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">simplifyGraph</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbCores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_NB_CORES</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">tru</span>e</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">fals</span>e</span><span class="p">;</span></span>
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">Simplifications</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Graph_type</span><span class="p">,</span><span class="n" style="color: #333;">Node</span><span class="p">,</span><span class="n" style="color: #333;">Edge</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">graphSimplifications</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">nbCores</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">saw</span><span class="p">(</span><span class="s" style="color: #d14;">"-no-tip-removal"</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="309" style="width: 35px; color: rgba(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="309" style="width: 35px; color: rgba(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">@@ -309,6 +309,7 @@ string Minia::assemble (/*const, removed because Simplifications isn't const any</td>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** We gather some statistics. */</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"stats"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"traversal"</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getStr</span><span class="p">(</span><span class="n" style="color: #333;">STR_TRAVERSAL_KIND</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"nb_solid_kmers"</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d"</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">_nbSolidKmers</span><span class="p">);</span></span>
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312
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<td class="diff-line-num new_line" data-linenumber="313" style="width: 35px; color: rgba(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="LC313" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"nb_contigs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d"</span><span class="p">,</span> <span class="n" style="color: #333;">nbContigs</span><span class="p">);</span></span>
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<td class="diff-line-num new_line" data-linenumber="314" style="width: 35px; color: rgba(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="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"nb_small_contigs_discarded"</span><span class="p">,</span><span class="s" style="color: #d14;">"%d"</span><span class="p">,</span> <span class="n" style="color: #333;">nbSmallContigs</span><span class="p">);</span></span>
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314
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<td class="diff-line-num new_line" data-linenumber="315" style="width: 35px; color: rgba(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="LC315" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"nt_assembled"</span><span class="p">,</span> <span class="s" style="color: #d14;">"%ld"</span><span class="p">,</span> <span class="n" style="color: #333;">totalNt</span><span class="p">);</span></span>
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