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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/abyss">Debian Med / abyss</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/abyss/commit/e2ac24df5fbe2bfbc5e90d8f8536715303bda141">e2ac24df</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-04-20T09:57:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.0</pre>
</li>
</ul>
<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
</a>
</li>
<li class="file-stats">
<a href="#5ee1a0badd939cd28079fd420acec1d3345c7315">
Common/ContigID.h
</a>
</li>
<li class="file-stats">
<a href="#e7569b923fbde824f301b50a4974c48d020ece83">
Common/Histogram.h
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<li class="file-stats">
<a href="#1b6ec911a8bc837df9a997656851685b42656362">
Common/IOUtil.h
</a>
</li>
<li class="file-stats">
<a href="#ca4eddc60f5842e58e0e33424515ff399c6acb6c">
Common/SAM.h
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<li class="file-stats">
<a href="#1fc758788ade2bc4050f14e6bc7b0eadd4ae2551">
MergePaths/MergePaths.cpp
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<li class="file-stats">
<a href="#cc89e9bae60f4855d94b92272217e92ebb5bcf52">
Misc/samtobreak.hs
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#b1b13c18220af2e50a75abece48a60734024e816">
Scaffold/longseqdist.cpp
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<li class="file-stats">
<a href="#9d80e70fb33c7d536a57c45a5a78da09933f9744">
Scaffold/scaffold.cc
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<li class="file-stats">
<a href="#b7e48c450c5b184961bbcd9c2328972a64067607">
SimpleGraph/SimpleGraph.cpp
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<li class="file-stats">
<a href="#cd06d399cbb97ac80091363ace10b558e194af5f">
bin/abyss-pe
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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<li class="file-stats">
<a href="#54545de904c655f7c6b1ed6e0f6e947540dbf202">
doc/ABYSS.1
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<li class="file-stats">
<a href="#210a6761e540ac8179e4a92fdffba66759a77e27">
doc/abyss-pe.1
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<li class="file-stats">
<a href="#58b9c1ec4a434e1b73496c894a35770e972461a5">
doc/abyss-tofastq.1
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</li>
</ul>
<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/abyss/commit/e2ac24df5fbe2bfbc5e90d8f8536715303bda141#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2017-12-19 Ben Vandervalk <benv@bcgsc.ca></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2018-04-13 Ben Vandervalk <benv@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 2.1.0</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Adds support for misassembly correction and scaffolding</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> using linked reads, using Tigmint and ARCS. (Tigmint and</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> ARCS must be installed separately.)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Support simultaneous optimization of `s` (min sequence length)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> and `n` (min supporting read pairs / Chromium barcodes)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> during scaffolding</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> abyss-longseqdist:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Fix hang on input SAM containing no alignments with MAPQ > 0</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> abyss-pe:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * New `lr` parameter. Provide linked reads (i.e. 10x Genomics</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> Chromium reads) via this parameter to perform misassembly</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> correction and scaffolding using Chromium barcode information.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> Requires Tigmint and ARCS tools to be installed in addition</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> to ABySS.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> * Fix bug where `j` (threads) was not being correctly passed to</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> to `bgzip`/`pigz`</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> * Fix bug where `zsh` time/memory profiling was not being used,</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> even when `zsh` was available</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> abyss-scaffold:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> * Simultaneous optimization of `n` and `s` using line search</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> or grid search [default]</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> SimpleGraph:</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> * add options `-s` and `-n` to filter paired-end paths by</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> seed length and edge weight, respectively</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">2018-03-14 Ben Vandervalk <benv@bcgsc.ca></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> * Release version 2.0.3</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> * Many compiler fixes for GCC >= 6, Boost >= 1.64</span>
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<li id="5ee1a0badd939cd28079fd420acec1d3345c7315">
<a href="https://salsa.debian.org/med-team/abyss/commit/e2ac24df5fbe2bfbc5e90d8f8536715303bda141#5ee1a0badd939cd28079fd420acec1d3345c7315"><strong>Common/ContigID.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,13 +24,32 @@ static inline void setNextContigName(cstring s)</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"> <span class="n" style="color: #333;">g_nextContigName</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Set the next contig name returned by createContigName</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * to one plus the current largest numeric contig name.</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setNextContigName</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g_contigNames</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">g_nextContigName</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">maxContigName</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">g_contigNames</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;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">cstring</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_contigNames</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istringstream</span> <span class="n" style="color: #333;">iss</span><span class="p">((</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</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="LC41" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">contigName</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">iss</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">contigName</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">iss</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">contigName</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxContigName</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">maxContigName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">contigName</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">g_nextContigName</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">maxContigName</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Return the next unique contig name. */</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">createContigName</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g_nextContigName</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">g_contigNames</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">setNextContigName</span><span class="p">(</span><span class="n" style="color: #333;">g_contigNames</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g_nextContigName</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="n" style="color: #333;">setNextContigName</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostringstream</span> <span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">g_nextContigName</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ss</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">();</span></span>
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<li id="e7569b923fbde824f301b50a4974c48d020ece83">
<a href="https://salsa.debian.org/med-team/abyss/commit/e2ac24df5fbe2bfbc5e90d8f8536715303bda141#e7569b923fbde824f301b50a4974c48d020ece83"><strong>Common/Histogram.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -315,6 +315,29 @@ namespace std {</td>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c"> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">Histogram</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">Histogram</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Print assembly contiguity statistics header. */</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">printContiguityStatsHeader</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minSize</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sep</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">expSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="c"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"n"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"n:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">minSize</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"L50"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">expSize</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"NG50"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"min"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"N80"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"N20"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"E-size"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"max"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"sum"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"name"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Print assembly contiguity statistics. */</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">printContiguityStats</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Histogram</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">h0</span><span class="p">,</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">@@ -323,22 +346,8 @@ static inline std::ostream& printContiguityStats(</td>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">expSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="c"> <span class="n" style="color: #333;">Histogram</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h0</span><span class="p">.</span><span class="n" style="color: #333;">trimLow</span><span class="p">(</span><span class="n" style="color: #333;">minSize</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">printHeader</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="c"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"n"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"n:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">minSize</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"L50"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">expSize</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="c"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"LG50"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"NG50"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="c"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"min"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"N80"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"N50"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"N20"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"E-size"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"max"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"sum"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"name"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="c"> <span class="p">}</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">printHeader</span><span class="p">)</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="c"> <span class="n" style="color: #333;">printContiguityStatsHeader</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">minSize</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="p">,</span> <span class="n" style="color: #333;">expSize</span><span class="p">);</span></span>
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342
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">n50</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">n50</span><span class="p">();</span></span>
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343
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352
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="c"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">toEng</span><span class="p">(</span><span class="n" style="color: #333;">h0</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;">sep</span></span>
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353
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">toEng</span><span class="p">(</span><span class="n" style="color: #333;">h</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;">sep</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">@@ -51,9 +51,12 @@ static inline std::istream& operator>>(std::istream& in, expect o)</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"> <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="s" style="color: #d14;">"error: Expected `"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' and saw "</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"> <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="sc" style="color: #d14;">'`'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"> <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="s" style="color: #d14;">"near: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <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="s" style="color: #d14;">"end-of-file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"> <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="s" style="color: #d14;">"I/O error</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/abyss/commit/e2ac24df5fbe2bfbc5e90d8f8536715303bda141#ca4eddc60f5842e58e0e33424515ff399c6acb6c"><strong>Common/SAM.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -275,6 +275,8 @@ struct SAMRecord : SAMAlignment {</td>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&=</span> <span class="o" style="font-weight: 600;">~</span><span class="p">(</span><span class="n" style="color: #333;">FPROPER_PAIR</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">FMUNMAP</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">FMREVERSE</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">FPAIRED</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rname</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">rname</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isReverse</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">isReverse</span><span class="p">())</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">FPROPER_PAIR</span><span class="p">;</span></span>
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278
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">isUnmapped</span><span class="p">())</span></span>
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279
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">FMUNMAP</span><span class="p">;</span></span>
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280
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">isReverse</span><span class="p">())</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="310" style="width: 35px; color: rgba(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">@@ -308,7 +310,7 @@ struct SAMRecord : SAMAlignment {</td>
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308
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="c"> <span class="n" style="color: #333;">friend</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">operator</span> <span class="o" style="font-weight: 600;"><<</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SAMRecord</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">o</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">qname</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="c"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">qname</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">flag</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">rname</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="318" style="width: 35px; color: rgba(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">@@ -316,13 +318,16 @@ struct SAMRecord : SAMAlignment {</td>
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316
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span></span>
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317
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">mrnm</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">rname</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;">o</span><span class="p">.</span><span class="n" style="color: #333;">mrnm</span><span class="p">)</span></span>
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">isize</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">isize</span><span class="p"><span class="idiff left right">;</span></span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if SAM_SEQ_QUAL</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="c"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">out</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">qual</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">tags</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="c"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">tags</span><span class="p">;</span></span>
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323
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="c"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*"</span><span class="p">;</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">out</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*"</span><span class="p">;</span></span>
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325
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="c"> <span class="n" style="color: #333;">friend</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">operator</span> <span class="o" style="font-weight: 600;">>></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">SAMRecord</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">o</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/abyss/commit/e2ac24df5fbe2bfbc5e90d8f8536715303bda141#1fc758788ade2bc4050f14e6bc7b0eadd4ae2551"><strong>MergePaths/MergePaths.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">@@ -58,6 +58,8 @@ static const char USAGE_MESSAGE[] =</td>
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58
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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59
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"><span class="s" style="color: #d14;">" -k, --kmer=KMER_SIZE k-mer size</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"><span class="s" style="color: #d14;">" -s, --seed-length=L minimum length of a seed contig [0]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"><span class="s" style="color: #d14;">" -G, --genome-size=N expected genome size. Used to calculate NG50</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"><span class="s" style="color: #d14;">" and associated stats [disabled]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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61
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"><span class="s" style="color: #d14;">" -o, --out=FILE write result to FILE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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62
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"><span class="s" style="color: #d14;">" --no-greedy use the non-greedy algorithm [default]</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="LC65" class="line" lang="cpp"><span class="s" style="color: #d14;">" --greedy use the greedy algorithm</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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">@@ -86,16 +88,20 @@ namespace opt {</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Use a greedy algorithm. */</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">greedy</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Genome size. Used to calculate NG50. */</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">genomeSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Write the path overlap graph to this file. */</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">graphPath</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">shortopts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"g:j:k:o:s:v"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">shortopts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">G:</span>g:j:k:o:s:v"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">OPT_HELP</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_VERSION</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_DB</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_LIBRARY</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_STRAIN</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_SPECIES</span> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//enum { OPT_HELP = 1, OPT_VERSION };</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">longopts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"genome-size"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'G'</span> <span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"graph"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'g'</span> <span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"greedy"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">greedy</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span> <span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"no-greedy"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">greedy</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span> <span class="p">},</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">@@ -135,6 +141,52 @@ static ContigPath align(const Lengths& lengths,</td>
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"></span>
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">gDebugPrint</span><span class="p">;</span></span>
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137
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Build a histogram of the lengths of the assembled paths and unused contigs.</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Note: This function does not account for the ammount of overlap between contigs.</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Histogram</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">buildAssembledLengthHistogram</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Lengths</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ContigPaths</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">paths</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">Histogram</span> <span class="n" style="color: #333;">h</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Compute the lengths of the paths</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Mark the vertices that are used in paths</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">used</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">ContigPaths</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">pathIt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paths</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">pathIt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">paths</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pathIt</span><span class="p">)</span> <span class="p">{</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ContigPath</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pathIt</span><span class="p">;</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">totalLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">ContigPath</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">it</span><span class="p">)</span> <span class="p">{</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ambiguous</span><span class="p">())</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">();</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">totalLength</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">used</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="p">}</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">totalLength</span><span class="p">);</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="p">}</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add the contigs that were not used in paths.</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lengths</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;">i</span><span class="p">)</span> <span class="p">{</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">used</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="p">}</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">h</span><span class="p">;</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"><span class="p">}</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Report assembly metrics. */</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">reportAssemblyMetrics</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Lengths</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ContigPaths</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">paths</span><span class="p">)</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"><span class="p">{</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">Histogram</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buildAssembledLengthHistogram</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="n" style="color: #333;">paths</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="185" 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">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">seedLen</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" 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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">printContiguityStats</span><span class="p">(</span><span class="n" style="color: #333;">cerr</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genomeSize</span><span class="p">)</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"><span class="p">}</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"></span>
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138
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Return all contigs that are tandem repeats, identified as those</span></span>
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139
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * contigs that appear more than once in a single path.</span></span>
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140
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="699" style="width: 35px; color: rgba(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="751" style="width: 35px; color: rgba(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">@@ -699,7 +751,7 @@ static void outputPathGraph(PathGraph& pathGraph)</td>
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699
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="cpp"><span class="p">}</span></span>
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700
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752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="cpp"></span>
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701
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753
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Sort and output the specified paths. */</span></span>
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702
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">outputSortedPaths</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ContigPathMap</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">paths</span><span class="p">)</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">outputSortedPaths</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">Lengths</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">ContigPathMap</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">paths</span><span class="p">)</span></span>
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703
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="cpp"><span class="p">{</span></span>
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704
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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Sort the paths.</span></span>
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705
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ContigPath</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sortedPaths</span><span class="p">(</span><span class="n" style="color: #333;">paths</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="715" style="width: 35px; color: rgba(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="767" style="width: 35px; color: rgba(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">@@ -715,6 +767,9 @@ static void outputSortedPaths(const ContigPathMap& paths)</td>
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715
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767
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="cpp"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sortedPaths</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">it</span><span class="p">)</span></span>
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716
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768
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">createContigName</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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717
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769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_good</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="cpp"></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Report assembly metrics.</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="cpp"> <span class="n" style="color: #333;">reportAssemblyMetrics</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="n" style="color: #333;">sortedPaths</span><span class="p">);</span></span>
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718
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="cpp"><span class="p">}</span></span>
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719
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774
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="cpp"></span>
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720
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775
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Assemble the path overlap graph. */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="753" style="width: 35px; color: rgba(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="808" style="width: 35px; color: rgba(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">@@ -753,7 +808,7 @@ static void assemblePathGraph(const Lengths& lengths,</td>
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753
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808
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Removing redundant contigs</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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754
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809
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="cpp"> <span class="n" style="color: #333;">removeSubsumedPaths</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="n" style="color: #333;">paths</span><span class="p">);</span></span>
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755
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="cpp"></span>
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756
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="cpp"> <span class="n" style="color: #333;">outputSortedPaths</span><span class="p">(</span><span class="n" style="color: #333;">paths</span><span class="p">);</span></span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="cpp"> <span class="n" style="color: #333;">outputSortedPaths</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">lengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">paths</span><span class="p">);</span></span>
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757
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812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="cpp"><span class="p">}</span></span>
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758
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813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="cpp"></span>
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759
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Read a set of paths from the specified file. */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="891" style="width: 35px; color: rgba(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="946" style="width: 35px; color: rgba(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">@@ -891,6 +946,12 @@ int main(int argc, char** argv)</td>
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891
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946
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<pre style="margin: 0;"> <span id="LC946" class="line" lang="cpp"> <span class="n" style="color: #333;">istringstream</span> <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">optarg</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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892
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947
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<pre style="margin: 0;"> <span id="LC947" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span></span>
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893
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<td class="diff-line-num new_line" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
948
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<pre style="margin: 0;"> <span id="LC948" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'?'</span><span class="p">:</span> <span class="n" style="color: #333;">die</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="949" 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">
949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'G'</span><span class="p">:</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genomeSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="cpp"> <span class="p">}</span></span>
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955
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<pre style="margin: 0;"> <span id="LC955" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'g'</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">graphPath</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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895
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956
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'j'</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">threads</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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896
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957
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'k'</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">k</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1051" style="width: 35px; color: rgba(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="1112" style="width: 35px; color: rgba(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">@@ -1051,7 +1112,7 @@ int main(int argc, char** argv)</td>
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1051
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1112
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<pre style="margin: 0;"> <span id="LC1112" class="line" lang="cpp"> <span class="p">}</span></span>
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1052
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1113
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<pre style="margin: 0;"> <span id="LC1113" class="line" lang="cpp"> <span class="n" style="color: #333;">originalPathMap</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1053
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1114
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<pre style="margin: 0;"> <span id="LC1114" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1054" class="line" lang="cpp"> <span class="n" style="color: #333;">outputSortedPaths</span><span class="p">(</span><span class="n" style="color: #333;">resultsPathMap</span><span class="p">);</span></span>
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1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="cpp"> <span class="n" style="color: #333;">outputSortedPaths</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">lengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">resultsPathMap</span><span class="p">);</span></span>
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1055
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="cpp"><span class="p">}</span></span>
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1118
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<pre style="margin: 0;"> <span id="LC1118" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/abyss/commit/e2ac24df5fbe2bfbc5e90d8f8536715303bda141#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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279
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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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280
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280
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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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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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282
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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.<span class="idiff left right">0.3</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="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.<span class="idiff left right">1.0</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="haskell"> <span class="n" style="color: #333;">usage</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Usage: samtobreak [OPTION]... [FILE]...</span><span class="se" style="color: #d14;">\n\</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="haskell"><span class="se" style="color: #d14;">\</span><span class="s" style="color: #d14;">Calculate contig and scaffold contiguity and correctness metrics.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="haskell"></span>
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<a href="https://salsa.debian.org/med-team/abyss/commit/e2ac24df5fbe2bfbc5e90d8f8536715303bda141#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,6 +18,7 @@ Contents</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Assembling a paired-end library</span><span class="p">](</span><span class="sx" style="color: #d14;">#assembling-a-paired-end-library</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Assembling multiple libraries</span><span class="p">](</span><span class="sx" style="color: #d14;">#assembling-multiple-libraries</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Scaffolding</span><span class="p">](</span><span class="sx" style="color: #d14;">#scaffolding</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Scaffolding with linked reads</span><span class="p">](</span><span class="sx" style="color: #d14;">#scaffolding-with-linked-reads</span><span class="p">)</span></span>
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21
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Rescaffolding with long sequences</span><span class="p">](</span><span class="sx" style="color: #d14;">#rescaffolding-with-long-sequences</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Assembling using a Bloom filter de Bruijn graph</span><span class="p">](</span><span class="sx" style="color: #d14;">#assembling-using-a-bloom-filter-de-bruijn-graph</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Assembling using a paired de Bruijn graph</span><span class="p">](</span><span class="sx" style="color: #d14;">#assembling-using-a-paired-de-bruijn-graph</span><span class="p">)</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">@@ -37,20 +38,29 @@ Contents</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Quick Start</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">===========</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Install ABySS on <span class="idiff left right">Debian or Ubuntu</span></span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Install ABySS on <span class="idiff left right">Linux</span></span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"><span class="idiff left right">R</span>un the command</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"><span class="idiff left">Install </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">Linuxbrew</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">http://linuxbrew.sh/</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">, and r</span>un the command</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="markdown"><span class="sb" style="color: #d14;"> sudo apt-get install abyss</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="sb" style="color: #d14;"> brew install brewsci/bio/abyss</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Install ABySS on macOS</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown">Install <span class="p">[</span><span class="nv" style="color: teal;">Homebrew</span><span class="p">](</span><span class="sx" style="color: #d14;">https://brew.sh/</span><span class="p">)</span>, and run the command</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"><span class="sb" style="color: #d14;"> brew install brewsci/bio/abyss</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Install ABySS on Windows</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown">Install <span class="p">[</span><span class="nv" style="color: teal;">Windows Subsystem for Linux</span><span class="p">](</span><span class="sx" style="color: #d14;">https://docs.microsoft.com/en-us/windows/wsl/</span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: teal;">Linuxbrew</span><span class="p">](</span><span class="sx" style="color: #d14;">http://linuxbrew.sh/</span><span class="p">)</span>, and run the command</span>
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45
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown">or download and install the</span>
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<td class="diff-line-num old old_line" data-linenumber="47" 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">
47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Debian package</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.bcgsc.ca/platform/bioinfo/software/abyss</span><span class="p">)</span>.</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="sb" style="color: #d14;"> brew install brewsci/bio/abyss</span></span>
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48
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" data-linenumber="49" 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">
49
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<td class="diff-line-num new_line old" data-linenumber="59" 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="LC49" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Install ABySS on <span class="idiff left right">Mac OS X</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Install ABySS on <span class="idiff left right">Debian or Ubuntu</span></span></span>
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50
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="51" 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">
51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"><span class="idiff left">Install </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">Homebrew</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">http://brew.sh/</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">, and run the commands</span></span>
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<td class="diff-line-num new new_line" data-linenumber="61" 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">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"><span class="idiff left right">Run the command</span></span>
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52
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"></span>
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53
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<td class="diff-line-num new_line old" data-linenumber="63" 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="LC53" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right">brew install homebrew/science/</span>abyss</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right">sudo apt-get install </span>abyss</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Assemble a small synthetic data set</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"></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">@@ -66,19 +76,37 @@ Install [Homebrew](http://brew.sh/), and run the commands</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Dependencies</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">============</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown">Dependencies may be installed using the package manager <span class="p">[</span><span class="nv" style="color: teal;">Homebrew</span><span class="p">](</span><span class="sx" style="color: #d14;">https://homebrew.sh</span><span class="p">)</span> on macOS and <span class="p">[</span><span class="nv" style="color: teal;">Linxubrew</span><span class="p">](</span><span class="sx" style="color: #d14;">http://linuxbrew.sh</span><span class="p">)</span> on Linux and Windows, using Windows Subsystem for Linux.</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown">ABySS requires a C++ compiler that supports</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">OpenMP</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.openmp.org</span><span class="p">)</span> such as <span class="p">[</span><span class="nv" style="color: teal;">GCC</span><span class="p">](</span><span class="sx" style="color: #d14;">http://gcc.gnu.org</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown">ABySS requires the following libraries:</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Boost</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.boost.org/</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Open MPI</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.open-mpi.org</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">sparsehash</span><span class="p">](</span><span class="sx" style="color: #d14;">https://code.google.com/p/sparsehash/</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">SQLite</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.sqlite.org/</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="markdown">ABySS requires a C++ compiler that supports</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">OpenMP</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.openmp.org</span><span class="p">)</span> such as <span class="p">[</span><span class="nv" style="color: teal;">GCC</span><span class="p">](</span><span class="sx" style="color: #d14;">http://gcc.gnu.org</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"><span class="sb" style="color: #d14;"> brew install boost open-mpi google-sparsehash</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown">ABySS will receive an error when compiling with Boost 1.51.0 or 1.52.0</span>
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80
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown">since they contain a bug. Later versions of Boost compile without error.</span>
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81
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Dependencies for linked reads</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: teal;">ARCS</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/bcgsc/arcs</span><span class="p">)</span> to scaffold</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: teal;">Tigmint</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/bcgsc/tigmint</span><span class="p">)</span> to correct assembly errors</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"><span class="sb" style="color: #d14;"> brew install brewsci/bio/arcs brewsci/bio/links</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Optional dependencies</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: teal;">pigz</span><span class="p">](</span><span class="sx" style="color: #d14;">https://zlib.net/pigz/</span><span class="p">)</span> for parallel gzip</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: teal;">samtools</span><span class="p">](</span><span class="sx" style="color: #d14;">https://samtools.github.io</span><span class="p">)</span> for reading BAM files</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: teal;">zsh</span><span class="p">](</span><span class="sx" style="color: #d14;">https://sourceforge.net/projects/zsh/</span><span class="p">)</span> for reporting time and memory usage</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"><span class="sb" style="color: #d14;"> brew install pigz samtools zsh</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Compiling ABySS from GitHub</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">===========================</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown"></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">@@ -142,8 +170,7 @@ usage, although it will build without. sparsehash should be found in</td>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="markdown"><span class="sb" style="color: #d14;"> ./configure CPPFLAGS=-I/usr/local/include</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="markdown">If SQLite is installed in non-default directories, its location can be</span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="markdown">specified to <span class="sb" style="color: #d14;">`configure`</span>:</span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="markdown">If the optional dependency SQLite is installed in non-default directories, its location can be specified to <span class="sb" style="color: #d14;">`configure`</span>:</span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="markdown"><span class="sb" style="color: #d14;"> ./configure --with-sqlite=/opt/sqlite3</span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="169" style="width: 35px; color: rgba(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="196" style="width: 35px; color: rgba(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">@@ -169,7 +196,7 @@ To assemble paired reads in two files named `reads1.fa` and</td>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="markdown"><span class="sb" style="color: #d14;">`reads2.fa`</span> into contigs in a file named <span class="sb" style="color: #d14;">`ecoli-contigs.fa`</span>, run the</span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="markdown">command:</span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe name=ecoli k=<span class="idiff left right">64</span> in='reads1.fa reads2.fa'</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe name=ecoli k=<span class="idiff left right">96</span> in='reads1.fa reads2.fa'</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="markdown">The parameter <span class="sb" style="color: #d14;">`in`</span> specifies the input files to read, which may be in</span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="markdown">FASTA, FASTQ, qseq, export, SRA, SAM or BAM format and compressed with</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="208" style="width: 35px; color: rgba(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="235" style="width: 35px; color: rgba(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">@@ -208,7 +235,7 @@ fragment libraries and single-end reads. Note that the names of the libraries</td>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="markdown">The command line to assemble this example data set is:</span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe k=<span class="idiff left right">64</span> name=ecoli lib='pea peb' \</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe k=<span class="idiff left right">96</span> name=ecoli lib='pea peb' \</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="markdown"><span class="sb" style="color: #d14;"> pea='pea_1.fa pea_2.fa' peb='peb_1.fa peb_2.fa' \</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="markdown"><span class="sb" style="color: #d14;"> se='se1.fa se2.fa'</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="228" style="width: 35px; color: rgba(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="255" style="width: 35px; color: rgba(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">@@ -228,13 +255,29 @@ Here's an example of assembling a data set with two paired-end</td>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="markdown">libraries and two mate-pair libraries. Note that the names of the libraries</span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="markdown">(<span class="sb" style="color: #d14;">`pea`</span>, <span class="sb" style="color: #d14;">`peb`</span>, <span class="sb" style="color: #d14;">`mpa`</span>, <span class="sb" style="color: #d14;">`mpb`</span>) are arbitrary.</span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe k=<span class="idiff left right">64</span> name=ecoli lib='pea peb' mp='mpc mpd' \</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe k=<span class="idiff left right">96</span> name=ecoli lib='pea peb' mp='mpc mpd' \</span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="markdown"><span class="sb" style="color: #d14;"> pea='pea_1.fa pea_2.fa' peb='peb_1.fa peb_2.fa' \</span></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="markdown"><span class="sb" style="color: #d14;"> mpc='mpc_1.fa mpc_2.fa' mpd='mpd_1.fa mpd_2.fa'</span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="markdown">The mate-pair libraries are used only for scaffolding and do not</span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="markdown">contribute towards the consensus sequence.</span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Scaffolding with linked reads</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">================================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="markdown">ABySS can scaffold using linked reads from 10x Genomics Chromium. The barcodes must first be extracted from the read sequences and added to the <span class="sb" style="color: #d14;">`BX:Z`</span> tag of the FASTQ header, typically using the <span class="sb" style="color: #d14;">`longranger basic`</span> command of <span class="p">[</span><span class="nv" style="color: teal;">Long Ranger</span><span class="p">](</span><span class="sx" style="color: #d14;">https://support.10xgenomics.com/genome-exome/software/overview/welcome</span><span class="p">)</span> or <span class="p">[</span><span class="nv" style="color: teal;">EMA preproc</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/arshajii/ema#readme</span><span class="p">)</span>. The linked reads are used to correct assembly errors, which requires that <span class="p">[</span><span class="nv" style="color: teal;">Tigmint</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/bcgsc/tigmint</span><span class="p">)</span>. The linked reads are also used for scaffolding, which requires <span class="p">[</span><span class="nv" style="color: teal;">ARCS</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/bcgsc/arcs</span><span class="p">)</span>. See <span class="p">[</span><span class="nv" style="color: teal;">Dependencies</span><span class="p">](</span><span class="sx" style="color: #d14;">#dependencies</span><span class="p">)</span> for installation instructions.</span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="markdown">ABySS can combine paired-end, mate-pair, and linked-read libraries. The <span class="sb" style="color: #d14;">`pe`</span> and <span class="sb" style="color: #d14;">`lr`</span> libraries will be used to build the de Bruijn graph. The <span class="sb" style="color: #d14;">`mp`</span> libraries will be used for paired-end/mate-pair scaffolding. The <span class="sb" style="color: #d14;">`lr`</span> libraries will be used for misassembly correction using Tigmint and scaffolding using ARCS.</span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe k=96 name=hsapiens \</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="markdown"><span class="sb" style="color: #d14;"> pe='pea' pea='lra.fastq.gz' \</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="markdown"><span class="sb" style="color: #d14;"> mp='mpa' mpa='lra.fastq.gz' \</span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="markdown"><span class="sb" style="color: #d14;"> lr='lra' lra='lra.fastq.gz'</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="markdown">ABySS performs better with a mixture of paired-end, mate-pair, and linked reads, but it is possible to assemble only linked reads using ABySS, though this mode of operation is experimental.</span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe k=96 name=hsapiens lr='lra' lra='lra.fastq.gz'</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Rescaffolding with long sequences</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=================================</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="247" style="width: 35px; color: rgba(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="290" style="width: 35px; color: rgba(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">@@ -247,7 +290,7 @@ Similar to scaffolding, the names of the datasets can be specified with</td>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="markdown">the <span class="sb" style="color: #d14;">`long`</span> parameter. These scaffolds will be stored in the file</span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="markdown"><span class="sb" style="color: #d14;">`${name}-long-scaffs.fa`</span>. The following is an example of an assembly with PET, MPET and an RNA-Seq assembly. Note that the names of the libraries are arbitrary.</span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe k=<span class="idiff left right">64</span> name=ecoli lib='pe1 pe2' mp='mp1 mp2' long='longa' \</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe k=<span class="idiff left right">96</span> name=ecoli lib='pe1 pe2' mp='mp1 mp2' long='longa' \</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="markdown"><span class="sb" style="color: #d14;"> pe1='pe1_1.fa pe1_2.fa' pe2='pe2_1.fa pe2_2.fa' \</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="markdown"><span class="sb" style="color: #d14;"> mp1='mp1_1.fa mp1_2.fa' mp2='mp2_1.fa mp2_2.fa' \</span></span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="markdown"><span class="sb" style="color: #d14;"> longa='longa.fa'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="266" style="width: 35px; color: rgba(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">@@ -266,7 +309,7 @@ example, the following will run a E. coli assembly with an overall memory budget</td>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="markdown">of 100 megabytes, 3 hash functions, a minimum k-mer count threshold of 3, with</span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="markdown">verbose logging enabled:</span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe name=ecoli k=<span class="idiff left right">64</span> in='reads1.fa reads2.fa' B=100M H=3 kc=3 v=-v</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe name=ecoli k=<span class="idiff left right">96</span> in='reads1.fa reads2.fa' B=100M H=3 kc=3 v=-v</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="markdown">At the current time, the user must calculate suitable values for <span class="sb" style="color: #d14;">`B`</span> and <span class="sb" style="color: #d14;">`H`</span> on</span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="markdown">their own, and finding the best value for <span class="sb" style="color: #d14;">`kc`</span> may require experimentation</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -291,7 +334,7 @@ To assemble using paired de Bruijn graph mode, specify both individual</td>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="markdown">k-mer size (<span class="sb" style="color: #d14;">`K`</span>) and k-mer pair span (<span class="sb" style="color: #d14;">`k`</span>). For example, to assemble E.</span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="markdown">coli with a individual k-mer size of 16 and a k-mer pair span of 64:</span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe name=ecoli K=16 k=<span class="idiff left right">64</span> in='reads1.fa reads2.fa'</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe name=ecoli K=16 k=<span class="idiff left right">96</span> in='reads1.fa reads2.fa'</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="markdown">In this example, the size of the intervening gap between k-mer pairs is</span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="markdown">32 bp (64 - 2<span class="se" style="color: #d14;">\*</span>16). Note that the <span class="sb" style="color: #d14;">`k`</span> parameter takes on a new meaning</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">@@ -308,7 +351,7 @@ respect to the original transcripts that were sequenced. In order to</td>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="markdown">run ABySS in strand-specific mode, the <span class="sb" style="color: #d14;">`SS`</span> parameter must be used as</span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="markdown">in the following example:</span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe name=SS-RNA k=<span class="idiff left right">64</span> in='reads1.fa reads2.fa' SS=--SS</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe name=SS-RNA k=<span class="idiff left right">96</span> in='reads1.fa reads2.fa' SS=--SS</span></span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="markdown">The expected orientation for the read sequences with respect to the</span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="markdown">original RNA is RF. i.e. the first read in a read pair is always in</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">@@ -406,6 +449,8 @@ Parameters of the driver script, `abyss-pe`</td>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`t`</span>: maximum length of blunt contigs to trim <span class="p">[</span><span class="nv" style="color: teal;">`k`</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`v`</span>: use <span class="sb" style="color: #d14;">`v=-v`</span> for verbose logging, <span class="sb" style="color: #d14;">`v=-vv`</span> for extra verbose</span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`x`</span>: spaced seed (Bloom filter assembly only)</span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`lr_s`</span>: minimum contig size required for building scaffolds with linked reads (bp) <span class="p">[</span><span class="nv" style="color: teal;">`S`</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`lr_n`</span>: minimum number of barcodes required for building scaffolds with linked reads <span class="p">[</span><span class="nv" style="color: teal;">`10`</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="markdown">Please see the</span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">abyss-pe</span><span class="p">](</span><span class="sx" style="color: #d14;">http://manpages.ubuntu.com/abyss-pe.1.html</span><span class="p">)</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">@@ -414,7 +459,7 @@ manual page for more information on assembly parameters.</td>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Environment variables</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=====================</span></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="markdown"><span class="sb" style="color: #d14;">`abyss-pe`</span> configuration variables may be set on the command line or from the environment, for example with <span class="sb" style="color: #d14;">`export k=<span class="idiff left right">20</span>`</span>. It can happen that <span class="sb" style="color: #d14;">`abyss-pe`</span> picks up such variables from your environment that you had not intended, and that can cause trouble. To troubleshoot that situation, use the <span class="sb" style="color: #d14;">`abyss-pe env`</span> command to print the values of all the <span class="sb" style="color: #d14;">`abyss-pe`</span> configuration variables:</span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="markdown"><span class="sb" style="color: #d14;">`abyss-pe`</span> configuration variables may be set on the command line or from the environment, for example with <span class="sb" style="color: #d14;">`export k=<span class="idiff left right">96</span>`</span>. It can happen that <span class="sb" style="color: #d14;">`abyss-pe`</span> picks up such variables from your environment that you had not intended, and that can cause trouble. To troubleshoot that situation, use the <span class="sb" style="color: #d14;">`abyss-pe env`</span> command to print the values of all the <span class="sb" style="color: #d14;">`abyss-pe`</span> configuration variables:</span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="markdown"><span class="sb" style="color: #d14;"> abyss-pe env [options]</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="markdown"></span>
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<li id="b1b13c18220af2e50a75abece48a60734024e816">
<a href="https://salsa.debian.org/med-team/abyss/commit/e2ac24df5fbe2bfbc5e90d8f8536715303bda141#b1b13c18220af2e50a75abece48a60734024e816"><strong>Scaffold/longseqdist.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">@@ -120,8 +120,7 @@ static void readAlignments(istream& in, Graph& g)</td>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">SAMRecord</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="n" style="color: #333;">prev</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">recs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">prev</span><span class="p">.</span><span class="n" style="color: #333;">isUnmapped</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">prev</span><span class="p">.</span><span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">prev</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">prev</span><span class="p">.</span><span class="n" style="color: #333;">isUnmapped</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">prev</span><span class="p">.</span><span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">prev</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">rec</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">isUnmapped</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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">@@ -6,6 +6,7 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "IOUtil.h"</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "Iterator.h"</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "Uncompress.h"</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "Common/UnorderedMap.h"</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "Graph/Assemble.h"</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "Graph/ContigGraph.h"</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "Graph/ContigGraphAlgorithms.h"</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">@@ -39,7 +40,7 @@ static const char VERSION_MESSAGE[] =</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="n" style="color: #333;">PROGRAM</span> <span class="s" style="color: #d14;">" ("</span> <span class="n" style="color: #333;">PACKAGE_NAME</span> <span class="s" style="color: #d14;">") "</span> <span class="n" style="color: #333;">VERSION</span> <span class="s" style="color: #d14;">"</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="LC41" class="line" lang="cpp"><span class="s" style="color: #d14;">"Written by Shaun Jackman.</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="LC42" class="line" lang="cpp"><span class="s" style="color: #d14;">"</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="LC42" class="line" lang="cpp"><span class="s" style="color: #d14;">"Copyright 201<span class="idiff left right">4</span> Canada's Michael Smith Genome Sciences Centre</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"><span class="s" style="color: #d14;">"Copyright 201<span class="idiff left right">8</span> Canada's Michael Smith Genome Sciences Centre</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">USAGE_MESSAGE</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"><span class="s" style="color: #d14;">"Usage: "</span> <span class="n" style="color: #333;">PROGRAM</span> <span class="s" style="color: #d14;">" -k<kmer> [OPTION]... FASTA|OVERLAP DIST...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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">@@ -54,9 +55,14 @@ static const char USAGE_MESSAGE[] =</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="s" style="color: #d14;">" Options:</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="LC56" class="line" lang="cpp"><span class="s" style="color: #d14;">"</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="LC57" class="line" lang="cpp"><span class="s" style="color: #d14;">" -n, --npairs=N minimum number of pairs [0]</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="LC57" class="line" lang="cpp"><span class="s" style="color: #d14;">" -s, --seed-length=N minimum contig length [200]</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="LC58" class="line" lang="cpp"><span class="s" style="color: #d14;">" or -s N0-N1 Find the value of s in [N0,N1]</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="LC58" class="line" lang="cpp"><span class="s" style="color: #d14;">" or -n A-B:S Find the value of n in [A,B] with step size S</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="LC59" class="line" lang="cpp"><span class="s" style="color: #d14;">" that maximizes the scaffold N50.</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="LC60" class="line" lang="cpp"><span class="s" style="color: #d14;">" Default value for the step size is 1, if unspecified.</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="LC61" class="line" lang="cpp"><span class="s" style="color: #d14;">" -s, --seed-length=N minimum contig length [1000]</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="LC62" class="line" lang="cpp"><span class="s" style="color: #d14;">" or -s A-B Find the value of s in [A,B]</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="LC63" class="line" lang="cpp"><span class="s" style="color: #d14;">" that maximizes the scaffold N50.</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="LC64" class="line" lang="cpp"><span class="s" style="color: #d14;">" --grid optimize using a grid search [default]</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="LC65" class="line" lang="cpp"><span class="s" style="color: #d14;">" --line optimize using a line search</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="LC66" class="line" lang="cpp"><span class="s" style="color: #d14;">" -k, --kmer=N length of a k-mer</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="LC67" class="line" lang="cpp"><span class="s" style="color: #d14;">" -G, --genome-size=N expected genome size. Used to calculate NG50</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="LC68" class="line" lang="cpp"><span class="s" style="color: #d14;">" and associated stats [disabled]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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">@@ -84,12 +90,17 @@ namespace opt {</td>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">k</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// used by ContigProperties</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Optimization search strategy. */</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">searchStrategy</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Minimum number of pairs. */</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minNumPairs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minEdgeWeightEnd</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minEdgeWeightStep</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"></span>
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90
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Minimum contig length. */</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minContigLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span>00</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minContigLengthEnd</span><span class="p">;</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minContigLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">10</span>00</span><span class="p">;</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minContigLengthEnd</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1000</span></span><span class="p">;</span></span>
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"></span>
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94
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Genome size. Used to calculate NG50. */</span></span>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">genomeSize</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="124" style="width: 35px; color: rgba(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="135" style="width: 35px; color: rgba(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">@@ -124,7 +135,9 @@ static const char shortopts[] = "G:g:k:n:o:s:v";</td>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"></span>
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">OPT_HELP</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_VERSION</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_MIN_GAP</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_MAX_GAP</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_COMP</span><span class="p">,</span></span>
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126
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">OPT_DB</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_LIBRARY</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_STRAIN</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_SPECIES</span> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//enum { OPT_HELP = 1, OPT_VERSION, OPT_MIN_GAP, OPT_MAX_GAP, OPT_COMP };</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Optimization search strategy. */</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">GRID_SEARCH</span><span class="p">,</span> <span class="n" style="color: #333;">LINE_SEARCH</span> <span class="p">};</span></span>
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128
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"></span>
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">longopts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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130
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"graph"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'g'</span> <span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -133,6 +146,8 @@ static const struct option longopts[] = {</td>
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133
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"min-gap"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_MIN_GAP</span> <span class="p">},</span></span>
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134
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"max-gap"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_MAX_GAP</span> <span class="p">},</span></span>
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135
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"npairs"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'n'</span> <span class="p">},</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"grid"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">searchStrategy</span><span class="p">,</span> <span class="n" style="color: #333;">GRID_SEARCH</span> <span class="p">},</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"line"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">searchStrategy</span><span class="p">,</span> <span class="n" style="color: #333;">LINE_SEARCH</span> <span class="p">},</span></span>
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136
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"out"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span> <span class="p">},</span></span>
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137
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"seed-length"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'s'</span> <span class="p">},</span></span>
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138
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"complex"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">comp_trans</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="171" style="width: 35px; color: rgba(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="186" style="width: 35px; color: rgba(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">@@ -171,16 +186,17 @@ struct InvalidEdge {</td>
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171
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"></span>
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172
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Return whether the specified edges has sufficient support. */</span></span>
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173
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">PoorSupport</span> <span class="p">{</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">PoorSupport</span><span class="p">(</span><span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p"><span class="idiff left">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m_g</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">g</span></span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">PoorSupport</span><span class="p">(</span><span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">minEdgeWeight</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m_g</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m_minEdgeWeight</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">minEdgeWeight</span></span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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175
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()(</span><span class="n" style="color: #333;">graph_traits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">edge_descriptor</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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176
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"> <span class="p">{</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_g</span><span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p">].</span><span class="n" style="color: #333;">numPairs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left">opt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">minNumPairs</span></span><span class="p">;</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_g</span><span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p">].</span><span class="n" style="color: #333;">numPairs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left right">m_minEdgeWeight</span></span><span class="p">;</span></span>
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178
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">m_g</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">m_minEdgeWeight</span><span class="p">;</span></span>
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"><span class="p">};</span></span>
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181
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp"></span>
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182
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Remove short vertices and unsupported edges from the graph. */</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">filterGraph</span><span class="p">(</span><span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minContigLength</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">filterGraph</span><span class="p">(</span><span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">min<span class="idiff left">EdgeWeight</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">min</span>ContigLength</span><span class="p">)</span></span>
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184
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"><span class="p">{</span></span>
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185
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">graph_traits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">GTraits</span><span class="p">;</span></span>
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186
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">GTraits</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vertex_descriptor</span> <span class="n" style="color: #333;">V</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="203" style="width: 35px; color: rgba(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="219" style="width: 35px; color: rgba(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">@@ -203,7 +219,7 @@ static void filterGraph(Graph& g, unsigned minContigLength)</td>
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203
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp"></span>
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204
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Remove poorly-supported edges.</span></span>
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205
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">numBefore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">num_edges</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">);</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">remove_edge_if</span><span class="p">(</span><span class="n" style="color: #333;">PoorSupport</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">),</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DG</span><span class="o" style="font-weight: 600;">&></span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">remove_edge_if</span><span class="p">(</span><span class="n" style="color: #333;">PoorSupport</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">minEdgeWeight</span></span><span class="p">),</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DG</span><span class="o" style="font-weight: 600;">&></span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">));</span></span>
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207
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">numRemovedE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numBefore</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">num_edges</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">);</span></span>
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208
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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209
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Removed "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">numRemovedE</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" edges.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="527" style="width: 35px; color: rgba(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="543" style="width: 35px; color: rgba(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">@@ -527,6 +543,8 @@ static ContigPath addDistEst(const Graph& g0, const Graph& g1,</td>
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527
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">ambiguous</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp"> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">E</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">e0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">edge</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">g0</span><span class="p">);</span></span>
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529
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545
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="cpp"> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">E</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">e1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">edge</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">);</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">e0</span><span class="p">.</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">e1</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC547" 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="s" style="color: #d14;">"error: missing edge: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">vertex_name</span><span class="p">,</span> <span class="n" style="color: #333;">g0</span><span class="p">,</span> <span class="n" style="color: #333;">u</span><span class="p">)</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;">get</span><span class="p">(</span><span class="n" style="color: #333;">vertex_name</span><span class="p">,</span> <span class="n" style="color: #333;">g0</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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530
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548
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">e0</span><span class="p">.</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">e1</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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549
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EP</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">e0</span><span class="p">.</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">g0</span><span class="p">[</span><span class="n" style="color: #333;">e0</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">e1</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isOverlap</span><span class="p">(</span><span class="n" style="color: #333;">ep</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="591" style="width: 35px; color: rgba(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="609" style="width: 35px; color: rgba(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">@@ -591,7 +609,10 @@ unsigned addLength(const Graph& g, It first, It last)</td>
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** A container of contig paths. */</span></span>
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ContigPath</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ContigPaths</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Build the scaffold length histogram. */</span></span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Build the scaffold length histogram.</span></span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param g The graph g is destroyed.</span></span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Histogram</span> <span class="nf" style="color: #900; font-weight: 600;">buildScaffoldLengthHistogram</span><span class="p">(</span></span>
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617
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="cpp"> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ContigPaths</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">paths</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -647,17 +668,45 @@ static void addCntgStatsToDb(</td>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Parameters of scaffolding. */</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">ScaffoldParam</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldParam</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">n</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">),</span> <span class="n" style="color: #333;">s</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">==</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScaffoldParam</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">o</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp"><span class="n" style="color: #333;">NAMESPACE_STD_HASH_BEGIN</span></span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><></span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">hash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ScaffoldParam</span><span class="o" style="font-weight: 600;">></span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScaffoldParam</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">param</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hash</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span><span class="p">()(</span><span class="n" style="color: #333;">param</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">hash</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span><span class="p">()(</span><span class="n" style="color: #333;">param</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="LC684" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"><span class="n" style="color: #333;">NAMESPACE_STD_HASH_END</span></span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Result of scaffolding. */</span></span>
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">ScaffoldResult</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">ScaffoldParam</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldResult</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">ScaffoldParam</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">n50</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldResult</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">n50</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">metrics</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">ScaffoldParam</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">),</span> <span class="n" style="color: #333;">n50</span><span class="p">(</span><span class="n" style="color: #333;">n50</span><span class="p">),</span> <span class="n" style="color: #333;">metrics</span><span class="p">(</span><span class="n" style="color: #333;">metrics</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">n50</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC694" 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;">string</span> <span class="n" style="color: #333;">metrics</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Build scaffold paths.</span></span>
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param output write the results</span></span>
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return the scaffold N50</span></span>
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">scaffold</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minContigLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="cpp"><span class="n" style="color: #333;">ScaffoldResult</span></span>
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">scaffold</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minContigLength</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="cpp"> <span class="n" style="color: #333;">Graph</span> <span class="n" style="color: #333;">g</span><span class="p">(</span><span class="n" style="color: #333;">g0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Filter the graph.</span></span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="cpp"> <span class="n" style="color: #333;">filterGraph</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">minContigLength</span><span class="p">);</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="cpp"> <span class="n" style="color: #333;">filterGraph</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">min<span class="idiff left">EdgeWeight</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">min</span>ContigLength</span><span class="p">);</span></span>
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710
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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711
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="cpp"> <span class="n" style="color: #333;">printGraphStats</span><span class="p">(</span><span class="n" style="color: #333;">cerr</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">);</span></span>
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712
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="cpp"></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">@@ -737,45 +786,198 @@ unsigned scaffold(const Graph& g0, unsigned minContigLength,</td>
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737
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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="cpp"> <span class="n" style="color: #333;">addToDb</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="p">,</span> <span class="s" style="color: #d14;">"scaffolds_assembled"</span><span class="p">,</span> <span class="n" style="color: #333;">paths</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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738
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787
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="cpp"> <span class="p">}</span></span>
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739
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="cpp"></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Output the paths.</span></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="cpp"> <span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">fout</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="cpp"> <span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</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;">cout</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fout</span><span class="p">;</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_good</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="cpp"> <span class="n" style="color: #333;">g_contigNames</span><span class="p">.</span><span class="n" style="color: #333;">unlock</span><span class="p">();</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ContigPath</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paths</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="cpp"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">paths</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">it</span><span class="p">)</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">createContigName</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">addDistEst</span><span class="p">(</span><span class="n" style="color: #333;">g0</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_good</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Output the graph.</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">graphPath</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="cpp"> <span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">out</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">graphPath</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_good</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">graphPath</span><span class="p">);</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="cpp"> <span class="n" style="color: #333;">write_dot</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">);</span></span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_good</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">graphPath</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Compute contiguity metrics.</span></span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLength</span><span class="p">;</span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" 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;">ostringstream</span> <span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="cpp"> <span class="n" style="color: #333;">Histogram</span> <span class="n" style="color: #333;">scaffold_histogram</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buildScaffoldLengthHistogram</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">paths</span><span class="p">);</span></span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="cpp"> <span class="n" style="color: #333;">printContiguityStats</span><span class="p">(</span><span class="n" style="color: #333;">ss</span><span class="p">,</span> <span class="n" style="color: #333;">scaffold_histogram</span><span class="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">,</span></span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genomeSize</span><span class="p">)</span></span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">n="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">minEdgeWeight</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" s="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">minContigLength</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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817
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<pre style="margin: 0;">+<span id="LC817" 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;">string</span> <span class="n" style="color: #333;">metrics</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ss</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">();</span></span>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="cpp"> <span class="n" style="color: #333;">addCntgStatsToDb</span><span class="p">(</span><span class="n" style="color: #333;">scaffold_histogram</span><span class="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">);</span></span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="cpp"></span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ScaffoldResult</span><span class="p">(</span><span class="n" style="color: #333;">minEdgeWeight</span><span class="p">,</span> <span class="n" style="color: #333;">minContigLength</span><span class="p">,</span></span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="cpp"> <span class="n" style="color: #333;">scaffold_histogram</span><span class="p">.</span><span class="n" style="color: #333;">trimLow</span><span class="p">(</span><span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">).</span><span class="n" style="color: #333;">n50</span><span class="p">(),</span></span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="cpp"> <span class="n" style="color: #333;">metrics</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="cpp"><span class="p">}</span></span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Memoize the optimization results so far. */</span></span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ScaffoldParam</span><span class="p">,</span> <span class="n" style="color: #333;">ScaffoldResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ScaffoldMemo</span><span class="p">;</span></span>
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827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="cpp"></span>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Build scaffold paths, memoized. */</span></span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="cpp"><span class="n" style="color: #333;">ScaffoldResult</span></span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">scaffold_memoized</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">ScaffoldMemo</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">memo</span><span class="p">)</span></span>
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831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="cpp"><span class="p">{</span></span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldParam</span> <span class="n" style="color: #333;">param</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldMemo</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memo</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="p">);</span></span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">memo</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Clear the metrics string, so that this result is not listed</span></span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// multiple times in the final table of metrics.</span></span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldResult</span> <span class="n" style="color: #333;">result</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">metrics</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="cpp"> <span class="p">}</span></span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="cpp"></span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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843
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<pre style="margin: 0;">+<span id="LC843" 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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Scaffolding with n="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" s="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldResult</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaffold</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="cpp"> <span class="n" style="color: #333;">memo</span><span class="p">[</span><span class="n" style="color: #333;">param</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="cpp"></span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Print assembly metrics.</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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849
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<pre style="margin: 0;">+<span id="LC849" 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="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLength</span><span class="p">;</span></span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="cpp"> <span class="n" style="color: #333;">printContiguityStatsHeader</span><span class="p">(</span><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="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genomeSize</span><span class="p">);</span></span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="cpp"> <span class="p">}</span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" 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;">result</span><span class="p">.</span><span class="n" style="color: #333;">metrics</span><span class="p">;</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="cpp"><span class="p">}</span></span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="cpp"></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Find the value of n that maximizes the scaffold N50. */</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">ScaffoldResult</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">optimize_n</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p">,</span></span>
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862
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<pre style="margin: 0;">+<span id="LC862" 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;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minContigLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldMemo</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">memo</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="cpp"><span class="p">{</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" 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;">string</span> <span class="n" style="color: #333;">metrics_table</span><span class="p">;</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">bestn</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bestN50</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeightStep</span><span class="p">)</span> <span class="p">{</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldResult</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaffold_memoized</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">minContigLength</span><span class="p">,</span> <span class="n" style="color: #333;">memo</span><span class="p">);</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="cpp"> <span class="n" style="color: #333;">metrics_table</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">metrics</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">n50</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bestN50</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="cpp"> <span class="n" style="color: #333;">bestN50</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">n50</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="cpp"> <span class="n" style="color: #333;">bestn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ScaffoldResult</span><span class="p">(</span><span class="n" style="color: #333;">bestn</span><span class="p">,</span> <span class="n" style="color: #333;">minContigLength</span><span class="p">,</span> <span class="n" style="color: #333;">bestN50</span><span class="p">,</span> <span class="n" style="color: #333;">metrics_table</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Find the value of s that maximizes the scaffold N50. */</span></span>
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">ScaffoldResult</span></span>
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">optimize_s</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC884" 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;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">minContigLength</span><span class="p">,</span></span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldMemo</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">memo</span><span class="p">)</span></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="cpp"><span class="p">{</span></span>
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887
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<pre style="margin: 0;">+<span id="LC887" 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;">string</span> <span class="n" style="color: #333;">metrics_table</span><span class="p">;</span></span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">bests</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bestN50</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">STEP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cbrt</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Three steps per decade.</span></span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">ilast</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span><span class="n" style="color: #333;">round</span><span class="p">(</span></span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">minContigLength</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">STEP</span><span class="p">));</span></span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span><span class="n" style="color: #333;">round</span><span class="p">(</span></span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">minContigLength</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">STEP</span><span class="p">));</span></span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">ilast</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">STEP</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="cpp"></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Round to 1 figure.</span></span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">nearestDecade</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">floor</span><span class="p">(</span><span class="n" style="color: #333;">log10</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)));</span></span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">(</span><span class="n" style="color: #333;">round</span><span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nearestDecade</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nearestDecade</span><span class="p">);</span></span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="cpp"></span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldResult</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaffold_memoized</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">memo</span><span class="p">);</span></span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="cpp"> <span class="n" style="color: #333;">metrics_table</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">metrics</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">n50</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bestN50</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="cpp"> <span class="n" style="color: #333;">bestN50</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">n50</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="cpp"> <span class="n" style="color: #333;">bests</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="cpp"> <span class="p">}</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ScaffoldResult</span><span class="p">(</span><span class="n" style="color: #333;">minEdgeWeight</span><span class="p">,</span> <span class="n" style="color: #333;">bests</span><span class="p">,</span> <span class="n" style="color: #333;">bestN50</span><span class="p">,</span> <span class="n" style="color: #333;">metrics_table</span><span class="p">);</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Find the values of n and s that maximizes the scaffold N50. */</span></span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">ScaffoldResult</span></span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">optimize_grid_search</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p">,</span></span>
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915
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<pre style="margin: 0;">+<span id="LC915" 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;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">,</span></span>
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916
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<pre style="margin: 0;">+<span id="LC916" 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;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">minContigLength</span><span class="p">)</span></span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="cpp"><span class="p">{</span></span>
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740
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918
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<pre style="margin: 0;"> <span id="LC918" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLength</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">output</span><span class="p">)</span> <span class="p">{</span></span>
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742
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<pre style="margin: 0;">-<span id="LC742" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">printHeader</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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743
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<pre style="margin: 0;">-<span id="LC743" class="line" lang="cpp"> <span class="n" style="color: #333;">Histogram</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buildScaffoldLengthHistogram</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">paths</span><span class="p">);</span></span>
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744
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="cpp"> <span class="n" style="color: #333;">printContiguityStats</span><span class="p">(</span><span class="n" style="color: #333;">cerr</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">,</span></span>
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745
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="cpp"> <span class="n" style="color: #333;">printHeader</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genomeSize</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">s="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">minContigLength</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="cpp"> <span class="n" style="color: #333;">printHeader</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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749
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="cpp"> <span class="n" style="color: #333;">addCntgStatsToDb</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">trimLow</span><span class="p">(</span><span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">).</span><span class="n" style="color: #333;">n50</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC752" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC753" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Output the paths.</span></span>
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<pre style="margin: 0;">-<span id="LC754" class="line" lang="cpp"> <span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">fout</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</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="LC755" class="line" lang="cpp"> <span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</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;">cout</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fout</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_good</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="cpp"> <span class="n" style="color: #333;">g_contigNames</span><span class="p">.</span><span class="n" style="color: #333;">unlock</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC758" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ContigPath</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paths</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="cpp"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">paths</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">it</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">createContigName</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span></span>
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">addDistEst</span><span class="p">(</span><span class="n" style="color: #333;">g0</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_good</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Output the graph.</span></span>
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<pre style="margin: 0;">-<span id="LC765" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">graphPath</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="cpp"> <span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">out</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">graphPath</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="LC767" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_good</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">graphPath</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="cpp"> <span class="n" style="color: #333;">write_dot</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_good</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">graphPath</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC771" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Print assembly contiguity statistics.</span></span>
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<pre style="margin: 0;">-<span id="LC773" class="line" lang="cpp"> <span class="n" style="color: #333;">Histogram</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buildScaffoldLengthHistogram</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">paths</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC774" class="line" lang="cpp"> <span class="n" style="color: #333;">printContiguityStats</span><span class="p">(</span><span class="n" style="color: #333;">cerr</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">,</span></span>
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775
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<pre style="margin: 0;">-<span id="LC775" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genomeSize</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">s="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">minContigLength</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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777
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<pre style="margin: 0;">-<span id="LC777" class="line" lang="cpp"> <span class="n" style="color: #333;">addCntgStatsToDb</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">);</span></span>
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778
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<pre style="margin: 0;">-<span id="LC778" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">trimLow</span><span class="p">(</span><span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">).</span><span class="n" style="color: #333;">n50</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="cpp"> <span class="n" style="color: #333;">printContiguityStatsHeader</span><span class="p">(</span><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="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genomeSize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="cpp"></span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldMemo</span> <span class="n" style="color: #333;">memo</span><span class="p">;</span></span>
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923
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<pre style="margin: 0;">+<span id="LC923" 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;">string</span> <span class="n" style="color: #333;">metrics_table</span><span class="p">;</span></span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldResult</span> <span class="n" style="color: #333;">best</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeightStep</span><span class="p">)</span> <span class="p">{</span></span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldResult</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optimize_s</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">minContigLength</span><span class="p">,</span> <span class="n" style="color: #333;">memo</span><span class="p">);</span></span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="cpp"> <span class="n" style="color: #333;">metrics_table</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">metrics</span><span class="p">;</span></span>
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928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">n50</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">n50</span><span class="p">)</span></span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="cpp"> <span class="n" style="color: #333;">best</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="cpp"> <span class="p">}</span></span>
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931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="cpp"></span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="cpp"> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">metrics</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metrics_table</span><span class="p">;</span></span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">best</span><span class="p">;</span></span>
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934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="cpp"><span class="p">}</span></span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="cpp"></span>
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936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Find the values of n and s that maximizes the scaffold N50. */</span></span>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">ScaffoldResult</span></span>
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938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">optimize_line_search</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p">,</span></span>
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939
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<pre style="margin: 0;">+<span id="LC939" 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;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC940" 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;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">minContigLength</span><span class="p">)</span></span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="cpp"><span class="p">{</span></span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLength</span><span class="p">;</span></span>
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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="cpp"> <span class="n" style="color: #333;">printContiguityStatsHeader</span><span class="p">(</span><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="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genomeSize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldMemo</span> <span class="n" style="color: #333;">memo</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC947" 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;">string</span> <span class="n" style="color: #333;">metrics_table</span><span class="p">;</span></span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldResult</span> <span class="n" style="color: #333;">best</span><span class="p">(</span></span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">minEdgeWeight</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="cpp"> <span class="n" style="color: #333;">minContigLength</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// An upper limit on the number of iterations.</span></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">MAX_ITERATIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">minEdgeWeight</span><span class="p">.</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeightStep</span><span class="p">;</span></span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MAX_ITERATIONS</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Optimize s.</span></span>
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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956
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<pre style="margin: 0;">+<span id="LC956" 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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Optimizing s for n="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="cpp"> <span class="n" style="color: #333;">printContiguityStatsHeader</span><span class="p">(</span><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="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genomeSize</span><span class="p">);</span></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="cpp"> <span class="p">}</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">previous_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="cpp"> <span class="n" style="color: #333;">best</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optimize_s</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">minContigLength</span><span class="p">,</span> <span class="n" style="color: #333;">memo</span><span class="p">);</span></span>
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961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="cpp"> <span class="n" style="color: #333;">metrics_table</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">metrics</span><span class="p">;</span></span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">previous_s</span><span class="p">)</span></span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="cpp"></span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Optimize n.</span></span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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967
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<pre style="margin: 0;">+<span id="LC967" 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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Optimizing n for s="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="cpp"> <span class="n" style="color: #333;">printContiguityStatsHeader</span><span class="p">(</span><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="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genomeSize</span><span class="p">);</span></span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="cpp"> <span class="p">}</span></span>
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970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">previous_n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="971" 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">
971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="cpp"> <span class="n" style="color: #333;">best</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optimize_n</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">,</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">memo</span><span class="p">);</span></span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="cpp"> <span class="n" style="color: #333;">metrics_table</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">metrics</span><span class="p">;</span></span>
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973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">previous_n</span><span class="p">)</span></span>
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974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="cpp"> <span class="p">}</span></span>
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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="cpp"></span>
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977
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<pre style="margin: 0;">+<span id="LC977" 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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Line search converged in "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">memo</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="s" style="color: #d14;">" iterations.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="979" 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">
979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="cpp"> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">metrics</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metrics_table</span><span class="p">;</span></span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">best</span><span class="p">;</span></span>
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779
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981
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<pre style="margin: 0;"> <span id="LC981" class="line" lang="cpp"><span class="p">}</span></span>
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780
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982
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<pre style="margin: 0;"> <span id="LC982" class="line" lang="cpp"></span>
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781
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983
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<pre style="margin: 0;"> <span id="LC983" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Run abyss-scaffold. */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -806,7 +1008,16 @@ int main(int argc, char** argv)</td>
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806
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1008
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<pre style="margin: 0;"> <span id="LC1008" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">graphPath</span><span class="p">;</span></span>
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807
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1009
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<pre style="margin: 0;"> <span id="LC1009" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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808
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1010
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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">:</span></span>
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809
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<pre style="margin: 0;">-<span id="LC809" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minNumPairs</span><span class="p">;</span></span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeight</span><span class="p">;</span></span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">expect</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeightEnd</span><span class="p">;</span></span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeight</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeightEnd</span><span class="p">);</span></span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeightEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeight</span><span class="p">;</span></span>
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1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">':'</span><span class="p">)</span></span>
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1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">expect</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeightStep</span><span class="p">;</span></span>
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1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeightStep</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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810
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1021
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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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811
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<td class="diff-line-num new_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1022
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<pre style="margin: 0;"> <span id="LC1022" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">:</span></span>
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812
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<td class="diff-line-num new_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="818" style="width: 35px; color: rgba(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="1029" style="width: 35px; color: rgba(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">@@ -818,7 +1029,8 @@ int main(int argc, char** argv)</td>
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818
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1029
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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">expect</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLengthEnd</span><span class="p">;</span></span>
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819
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<td class="diff-line-num new_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1030
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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLength</span></span>
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820
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<td class="diff-line-num new_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1031
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<pre style="margin: 0;"> <span id="LC1031" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLengthEnd</span><span class="p">);</span></span>
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821
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<td class="diff-line-num new_line old" data-linenumber="1032" 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="LC821" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLengthEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLength</span><span class="p">;</span></span>
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1034
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<pre style="margin: 0;"> <span id="LC1034" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1035
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<pre style="margin: 0;"> <span id="LC1035" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'v'</span><span class="p">:</span></span>
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1036
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<pre style="margin: 0;"> <span id="LC1036" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</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">@@ -908,37 +1120,51 @@ int main(int argc, char** argv)</td>
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1120
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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span></span>
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1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="cpp"> <span class="n" style="color: #333;">addToDb</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="p">,</span> <span class="s" style="color: #d14;">"Edges_invalid"</span><span class="p">,</span> <span class="n" style="color: #333;">numRemoved</span><span class="p">);</span></span>
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1122
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<pre style="margin: 0;"> <span id="LC1122" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC911" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLengthEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC912" class="line" lang="cpp"> <span class="n" style="color: #333;">scaffold</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLength</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC913" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC914" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC915" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC916" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Find the value of s that maximizes the scaffold N50.</span></span>
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<pre style="margin: 0;">-<span id="LC917" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">bests</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bestN50</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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918
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<pre style="margin: 0;">-<span id="LC918" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">STEP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cbrt</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Three steps per decade.</span></span>
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<pre style="margin: 0;">-<span id="LC919" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">ilast</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span><span class="n" style="color: #333;">round</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC920" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLengthEnd</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">STEP</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC921" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span><span class="n" style="color: #333;">round</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC922" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLength</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">STEP</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC923" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">ilast</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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924
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<pre style="margin: 0;">-<span id="LC924" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">STEP</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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925
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<pre style="margin: 0;">-<span id="LC925" class="line" lang="cpp"></span>
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926
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<pre style="margin: 0;">-<span id="LC926" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Round to 1 figure.</span></span>
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927
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<pre style="margin: 0;">-<span id="LC927" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">nearestDecade</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">floor</span><span class="p">(</span><span class="n" style="color: #333;">log10</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="928" 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">
928
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<pre style="margin: 0;">-<span id="LC928" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">(</span><span class="n" style="color: #333;">round</span><span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nearestDecade</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nearestDecade</span><span class="p">);</span></span>
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1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLength</span><span class="p">;</span></span>
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1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeight</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeightEnd</span></span>
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1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLength</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLengthEnd</span><span class="p">)</span> <span class="p">{</span></span>
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1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldResult</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaffold</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeight</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLength</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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1127
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Print assembly contiguity statistics.</span></span>
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1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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1129
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<pre style="margin: 0;">+<span id="LC1129" 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="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1130" 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">
1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="cpp"> <span class="n" style="color: #333;">printContiguityStatsHeader</span><span class="p">(</span><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="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genomeSize</span><span class="p">);</span></span>
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1131
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<pre style="margin: 0;">+<span id="LC1131" 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;">result</span><span class="p">.</span><span class="n" style="color: #333;">metrics</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1132" 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">
1132
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1133" 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">
1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldResult</span> <span class="n" style="color: #333;">best</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">searchStrategy</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1135" 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">
1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">GRID_SEARCH</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1136" 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">
1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="cpp"> <span class="n" style="color: #333;">best</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optimize_grid_search</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1137" 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">
1137
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<pre style="margin: 0;">+<span id="LC1137" 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;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeight</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeightEnd</span><span class="p">),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1138" 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">
1138
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<pre style="margin: 0;">+<span id="LC1138" 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;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLength</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLengthEnd</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1139" 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">
1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1140" 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">
1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">LINE_SEARCH</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1141" 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">
1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="cpp"> <span class="n" style="color: #333;">best</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optimize_line_search</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span></span>
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1142
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<pre style="margin: 0;">+<span id="LC1142" 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;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeight</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeightEnd</span><span class="p">),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1143" 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">
1143
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<pre style="margin: 0;">+<span id="LC1143" 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;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLength</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minContigLengthEnd</span><span class="p">));</span></span>
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1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="cpp"> <span class="nl">default:</span></span>
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1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="cpp"> <span class="n" style="color: #333;">abort</span><span class="p">();</span></span>
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1147
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1148" 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">
1148
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="cpp"> <span class="p">}</span></span>
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929
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1149
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<pre style="margin: 0;"> <span id="LC1149" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="930" 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">
930
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<td class="diff-line-num new_line old" data-linenumber="1150" 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="LC930" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">n50</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaffold</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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931
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1150
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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="932" 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">
932
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<td class="diff-line-num new_line old" data-linenumber="1151" 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="LC932" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="933" 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">
933
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<pre style="margin: 0;">-<span id="LC933" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n50</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bestN50</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="934" 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">
934
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<pre style="margin: 0;">-<span id="LC934" class="line" lang="cpp"> <span class="n" style="color: #333;">bestN50</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n50</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="935" 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">
935
</td>
<td class="diff-line-num new_line old" data-linenumber="1151" 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="LC935" class="line" lang="cpp"> <span class="n" style="color: #333;">bests</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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1151
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<pre style="margin: 0;">+<span id="LC1151" 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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Scaffolding with n="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" s="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="cpp"> <span class="n" style="color: #333;">ScaffoldResult</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaffold</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Print the table of all the parameter values attempted and their metrics.</span></span>
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1156" 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="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="cpp"> <span class="n" style="color: #333;">printContiguityStatsHeader</span><span class="p">(</span><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="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genomeSize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1158" 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;">best</span><span class="p">.</span><span class="n" style="color: #333;">metrics</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1159" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC937" class="line" lang="cpp"> <span class="p">}</span></span>
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1160
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<pre style="margin: 0;"> <span id="LC1160" class="line" lang="cpp"></span>
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939
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<pre style="margin: 0;">-<span id="LC939" class="line" lang="cpp"> <span class="n" style="color: #333;">bestN50</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaffold</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">bests</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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940
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<td class="diff-line-num new_line old" data-linenumber="1161" 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="LC940" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Best scaffold N50 is "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bestN50</span></span>
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941
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<pre style="margin: 0;">-<span id="LC941" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" at s="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bests</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">".</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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1161
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<pre style="margin: 0;">+<span id="LC1161" 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="sc" style="color: #d14;">'\n'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Best scaffold N50 is "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">n50</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" at n="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" s="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">best</span><span class="p">.</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">".</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="cpp"></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Print assembly contiguity statistics.</span></span>
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1164
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<pre style="margin: 0;">+<span id="LC1164" 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="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1165" class="line" lang="cpp"> <span class="n" style="color: #333;">printContiguityStatsHeader</span><span class="p">(</span><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="p">,</span> <span class="n" style="color: #333;">STATS_MIN_LENGTH</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genomeSize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1166" 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;">result</span><span class="p">.</span><span class="n" style="color: #333;">metrics</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="cpp"> <span class="p">}</span></span>
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1168
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<pre style="margin: 0;"> <span id="LC1168" class="line" lang="cpp"></span>
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943
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1169
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<pre style="margin: 0;"> <span id="LC1169" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1170
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<pre style="margin: 0;"> <span id="LC1170" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/abyss/commit/e2ac24df5fbe2bfbc5e90d8f8536715303bda141#b7e48c450c5b184961bbcd9c2328972a64067607"><strong>SimpleGraph/SimpleGraph.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">@@ -30,7 +30,7 @@ static const char VERSION_MESSAGE[] =</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="n" style="color: #333;">PROGRAM</span> <span class="s" style="color: #d14;">" ("</span> <span class="n" style="color: #333;">PACKAGE_NAME</span> <span class="s" style="color: #d14;">") "</span> <span class="n" style="color: #333;">VERSION</span> <span class="s" style="color: #d14;">"</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="LC31" class="line" lang="cpp"><span class="s" style="color: #d14;">"Written by Jared Simpson and Shaun Jackman.</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="LC32" class="line" lang="cpp"><span class="s" style="color: #d14;">"</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="LC33" class="line" lang="cpp"><span class="s" style="color: #d14;">"Copyright 201<span class="idiff left right">4</span> Canada's Michael Smith Genome Sciences Centre</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="s" style="color: #d14;">"Copyright 201<span class="idiff left right">8</span> Canada's Michael Smith Genome Sciences Centre</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">USAGE_MESSAGE</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="s" style="color: #d14;">"Usage: "</span> <span class="n" style="color: #333;">PROGRAM</span> <span class="s" style="color: #d14;">" -k<kmer> -o<out.path> [OPTION]... ADJ DIST</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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">@@ -44,6 +44,8 @@ static const char USAGE_MESSAGE[] =</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"><span class="s" style="color: #d14;">" Options:</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="LC45" class="line" lang="cpp"><span class="s" style="color: #d14;">"</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="LC46" class="line" lang="cpp"><span class="s" style="color: #d14;">" -k, --kmer=KMER_SIZE k-mer size</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="LC47" class="line" lang="cpp"><span class="s" style="color: #d14;">" -n, --npairs=N minimum number of pairs [0]</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="LC48" class="line" lang="cpp"><span class="s" style="color: #d14;">" -s, --seed-length=N minimum seed contig length [0]</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="LC49" class="line" lang="cpp"><span class="s" style="color: #d14;">" -d, --dist-error=N acceptable error of a distance estimate</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="LC50" class="line" lang="cpp"><span class="s" style="color: #d14;">" default is 6 bp</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="LC51" class="line" lang="cpp"><span class="s" style="color: #d14;">" --max-cost=COST maximum computational cost</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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 +75,12 @@ namespace opt {</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Minimum number of pairs. */</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Minimum seed length. */</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minSeedLength</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** The acceptable error of a distance estimate. */</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">distanceError</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"></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">@@ -80,7 +88,7 @@ namespace opt {</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DIST</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// used by Estimate</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">shortopts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"d:j:k:<span class="idiff left right">o</span>:v"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">shortopts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"d:j:k:<span class="idiff left right">n:o:s</span>:v"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">OPT_HELP</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_VERSION</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_MAX_COST</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">OPT_DB</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_LIBRARY</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_STRAIN</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_SPECIES</span> <span class="p">};</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,6 +96,8 @@ enum { OPT_HELP = 1, OPT_VERSION, OPT_MAX_COST,</td>
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<td class="diff-line-num old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
88
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<td class="diff-line-num new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
89
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<td class="diff-line-num new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">longopts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
90
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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"kmer"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'k'</span> <span class="p">},</span></span>
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<td class="diff-line-num new old_line" data-linenumber="91" 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="99" 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">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"npairs"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'n'</span> <span class="p">},</span></span>
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<td class="diff-line-num new old_line" data-linenumber="91" 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="100" 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">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"seed-length"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'s'</span> <span class="p">},</span></span>
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<td class="diff-line-num old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
91
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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"dist-error"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'d'</span> <span class="p">},</span></span>
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<td class="diff-line-num old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
92
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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"max-cost"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_MAX_COST</span> <span class="p">},</span></span>
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<td class="diff-line-num old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
93
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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"out"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span> <span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="125" style="width: 35px; color: rgba(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="135" style="width: 35px; color: rgba(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">@@ -125,7 +135,9 @@ int main(int argc, char** argv)</td>
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<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
125
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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'j'</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">threads</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
126
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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'k'</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">k</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
127
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<td class="diff-line-num new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">OPT_MAX_COST</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">maxCost</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="128" 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="138" 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">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeight</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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128
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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'s'</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minSeedLength</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
129
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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'v'</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
130
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<td class="diff-line-num new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">OPT_HELP</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
131
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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">USAGE_MESSAGE</span><span class="p">;</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">@@ -248,6 +260,9 @@ static unsigned g_minNumPairs = UINT_MAX;</td>
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">g_minNumPairsUsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">UINT_MAX</span><span class="p">;</span></span>
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249
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"></span>
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250
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="p">{</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">seedTooShort</span><span class="p">;</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">noEdges</span><span class="p">;</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">edgesRemoved</span><span class="p">;</span></span>
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251
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">totalAttempted</span><span class="p">;</span></span>
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">uniqueEnd</span><span class="p">;</span></span>
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253
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">noPossiblePaths</span><span class="p">;</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">@@ -631,6 +646,16 @@ static void handleEstimate(const Graph& g,</td>
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646
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="cpp"> <span class="n" style="color: #333;">pthread_mutex_unlock</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">coutMutex</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="cpp"><span class="p">}</span></span>
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648
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Return whether the specified edge has sufficient support. */</span></span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">PoorSupport</span> <span class="p">{</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="cpp"> <span class="n" style="color: #333;">PoorSupport</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minEdgeWeight</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">m_minEdgeWeight</span><span class="p">(</span><span class="n" style="color: #333;">minEdgeWeight</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Estimates</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;">estimate</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="cpp"> <span class="p">{</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">estimate</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">numPairs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m_minEdgeWeight</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">m_minEdgeWeight</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">WorkerArg</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="cpp"> <span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">in</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="cpp"> <span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out</span><span class="p">;</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">@@ -642,6 +667,9 @@ struct WorkerArg {</td>
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">worker</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pArg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp"> <span class="n" style="color: #333;">WorkerArg</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">WorkerArg</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">pArg</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">countSeedTooShort</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">countNoEdges</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">countEdgesRemoved</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;;)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Lock the input stream. */</span></span>
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">pthread_mutex_t</span> <span class="n" style="color: #333;">inMutex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PTHREAD_MUTEX_INITIALIZER</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="679" style="width: 35px; color: rgba(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">@@ -651,6 +679,26 @@ static void* worker(void* pArg)</td>
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="cpp"> <span class="n" style="color: #333;">pthread_mutex_unlock</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">inMutex</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">good</span><span class="p">)</span></span>
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681
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">graph</span><span class="p">)[</span><span class="n" style="color: #333;">ContigNode</span><span class="p">(</span><span class="n" style="color: #333;">er</span><span class="p">.</span><span class="n" style="color: #333;">refID</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)].</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minSeedLength</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">countSeedTooShort</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Remove edges with insufficient support.</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"> <span class="n" style="color: #333;">Estimates</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">estimates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">er</span><span class="p">.</span><span class="n" style="color: #333;">estimates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">estimates</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">sizeBefore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">estimates</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"> <span class="n" style="color: #333;">estimates</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="cpp"> <span class="n" style="color: #333;">remove_if</span><span class="p">(</span><span class="n" style="color: #333;">estimates</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">estimates</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">PoorSupport</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minEdgeWeight</span><span class="p">)),</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp"> <span class="n" style="color: #333;">estimates</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">sizeAfter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">estimates</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">edgesRemoved</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sizeBefore</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sizeAfter</span><span class="p">;</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp"> <span class="n" style="color: #333;">countEdgesRemoved</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">edgesRemoved</span><span class="p">;</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sizeAfter</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">countNoEdges</span><span class="p">;</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="cpp"> <span class="p">}</span></span>
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702
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="cpp"></span>
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655
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703
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Flip the anterior distance estimates.</span></span>
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656
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704
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">Estimates</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">er</span><span class="p">.</span><span class="n" style="color: #333;">estimates</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="673" style="width: 35px; color: rgba(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="721" style="width: 35px; color: rgba(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">@@ -673,6 +721,14 @@ static void* worker(void* pArg)</td>
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673
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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="cpp"> <span class="n" style="color: #333;">pthread_mutex_unlock</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">outMutex</span><span class="p">);</span></span>
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674
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="cpp"> <span class="p">}</span></span>
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675
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723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="cpp"> <span class="p">}</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp"></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">pthread_mutex_t</span> <span class="n" style="color: #333;">statsMutex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PTHREAD_MUTEX_INITIALIZER</span><span class="p">;</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="cpp"> <span class="n" style="color: #333;">pthread_mutex_lock</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">statsMutex</span><span class="p">);</span></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="cpp"> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">seedTooShort</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">countSeedTooShort</span><span class="p">;</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="cpp"> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">noEdges</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">countNoEdges</span><span class="p">;</span></span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="cpp"> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">edgesRemoved</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">countEdgesRemoved</span><span class="p">;</span></span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="cpp"> <span class="n" style="color: #333;">pthread_mutex_unlock</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">statsMutex</span><span class="p">);</span></span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="cpp"></span>
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676
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732
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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677
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733
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="cpp"><span class="p">}</span></span>
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678
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734
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="707" style="width: 35px; color: rgba(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="763" style="width: 35px; color: rgba(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">@@ -707,6 +763,9 @@ static void generatePathsThroughEstimates(const Graph& g,</td>
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707
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763
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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708
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="cpp"></span>
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709
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span></span>
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<td class="diff-line-num new new_line" data-linenumber="766" 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">
766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Seed too short: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">seedTooShort</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="710" 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="767" 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">
767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Seeds with no edges: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">noEdges</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="710" 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="768" 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">
768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Edges removed: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">edgesRemoved</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num old_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
710
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<td class="diff-line-num new_line" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Total paths attempted: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">totalAttempted</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num old_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
711
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<td class="diff-line-num new_line" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
770
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC770" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Unique path: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">uniqueEnd</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</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="LC771" class="line" lang="cpp"> <span class="s" style="color: #d14;">"No possible paths: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">noPossiblePaths</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<a href="https://salsa.debian.org/med-team/abyss/commit/e2ac24df5fbe2bfbc5e90d8f8536715303bda141#cd06d399cbb97ac80091363ace10b558e194af5f"><strong>bin/abyss-pe</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">@@ -3,14 +3,22 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Written by Shaun Jackman <sjackman@bcgsc.ca> and</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Anthony Raymond <traymond@bcgsc.ca>.</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="make"><span class="nv" style="color: teal;">SHELL</span><span class="o" style="font-weight: 600;">=</span>bash <span class="nt" style="color: navy;">-e</span> <span class="nt" style="color: navy;">-o</span> pipefail</span>
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6
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifneq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(shell</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">command</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-v</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">zsh),)</span></span>
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7
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Set pipefail to ensure that all commands of a pipe succeed.</span></span>
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8
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="nv" style="color: teal;">SHELL</span><span class="o" style="font-weight: 600;">=</span>zsh <span class="nt" style="color: navy;">-e</span> <span class="nt" style="color: navy;">-o</span> pipefail</span>
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9
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Report run time and memory usage with zsh.</span></span>
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10
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">REPORTTIME</span><span class="o" style="font-weight: 600;">=</span>1</span>
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11
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">TIMEFMT</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">time </span><span class="nv" style="color: teal;">user</span><span class="o" style="font-weight: 600;">=</span>%U <span class="nv" style="color: teal;">system</span><span class="o" style="font-weight: 600;">=</span>%S <span class="nv" style="color: teal;">elapsed</span><span class="o" style="font-weight: 600;">=</span>%E <span class="nv" style="color: teal;">cpu</span><span class="o" style="font-weight: 600;">=</span>%P <span class="nv" style="color: teal;">memory</span><span class="o" style="font-weight: 600;">=</span>%M <span class="nv" style="color: teal;">job</span><span class="o" style="font-weight: 600;">=</span>%J</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Record run time and memory usage in a file using GNU time.</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">time</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifneq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(shell</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">command</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-v</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">gtime),)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="make"><span class="nv" style="color: teal;">gtime</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">command </span>gtime <span class="nt" style="color: navy;">-v</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$@</span>.time</span>
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12
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="make"><span class="nv" style="color: teal;">SHELL</span><span class="o" style="font-weight: 600;">=</span>bash <span class="nt" style="color: navy;">-e</span> <span class="nt" style="color: navy;">-o</span> pipefail</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"><span class="nv" style="color: teal;">gtime</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">command time</span> <span class="nt" style="color: navy;">-v</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$@</span>.time</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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14
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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15
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"></span>
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16
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Define this environment variable on Mac OS X to read</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -93,10 +101,10 @@ endif</td>
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93
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="make"></span>
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94
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Use pigz or bgzip for parallel compression if available.</span></span>
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95
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifneq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(shell</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">command</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-v</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">pigz),)</span></span>
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96
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<td class="diff-line-num new_line old" data-linenumber="104" 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="LC96" class="line" lang="make"><span class="nv" style="color: teal;">gzip</span><span class="o" style="font-weight: 600;">=</span>pigz <span class="nt" style="color: navy;">-p</span><span class="nv" style="color: teal;">$<span class="idiff left right">t</span></span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="make"><span class="nv" style="color: teal;">gzip</span><span class="o" style="font-weight: 600;">=</span>pigz <span class="nt" style="color: navy;">-p</span><span class="nv" style="color: teal;">$<span class="idiff left right">j</span></span></span>
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97
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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98
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifneq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(shell</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">command</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-v</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">bgzip),)</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="make"><span class="nv" style="color: teal;">gzip</span><span class="o" style="font-weight: 600;">=</span>bgzip -@<span class="nv" style="color: teal;">$<span class="idiff left right">t</span></span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="make"><span class="nv" style="color: teal;">gzip</span><span class="o" style="font-weight: 600;">=</span>bgzip -@<span class="nv" style="color: teal;">$<span class="idiff left right">j</span></span></span>
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100
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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101
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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="make"><span class="nv" style="color: teal;">gzip</span><span class="o" style="font-weight: 600;">=</span>gzip</span>
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102
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="123" style="width: 35px; color: rgba(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="131" style="width: 35px; color: rgba(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">@@ -123,6 +131,13 @@ MARKDOWN=pandoc</td>
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123
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="make"></span>
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124
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="make"><span class="nv" style="color: teal;">map</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>foreach a,<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>2<span class="o" style="font-weight: 600;">)</span>,<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>call <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>1<span class="o" style="font-weight: 600;">)</span>,<span class="nv" style="color: teal;">$(a)</span><span class="o" style="font-weight: 600;">))</span></span>
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125
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="make"><span class="nv" style="color: teal;">deref</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: teal;">$1</span><span class="o" style="font-weight: 600;">)</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="make"></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">lr</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifndef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">lib</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="make"><span class="nv" style="color: teal;">lib</span><span class="o" style="font-weight: 600;">:=</span><span class="nv" style="color: teal;">$(pe)</span> <span class="nv" style="color: teal;">$(lr)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="make"></span>
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126
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">lib</span></span>
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127
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="make"><span class="nv" style="color: teal;">in</span><span class="o" style="font-weight: 600;">?=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>call map, deref, <span class="nv" style="color: teal;">$(lib)</span><span class="o" style="font-weight: 600;">)</span></span>
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128
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -131,6 +146,7 @@ lib?=$(name)</td>
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131
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">$(lib)?=$(in)</span></span>
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132
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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133
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="make"></span>
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134
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="make"><span class="nv" style="color: teal;">pe</span><span class="o" style="font-weight: 600;">?=</span><span class="nv" style="color: teal;">$(lib)</span></span>
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135
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="make"><span class="nv" style="color: teal;">mp</span><span class="o" style="font-weight: 600;">?=</span><span class="nv" style="color: teal;">$(pe)</span></span>
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136
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="make"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="157" style="width: 35px; color: rgba(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">@@ -141,6 +157,9 @@ endif</td>
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141
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">se</span></span>
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142
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="make"><span class="nl">override se</span><span class="o" style="font-weight: 600;">:</span><span class="nf" style="color: #900; font-weight: 600;">=$(strip $(se))</span></span>
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143
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">lr</span></span>
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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">override</span> <span class="nv" style="color: teal;">lr_reads</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>strip <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>call map, deref, <span class="nv" style="color: teal;">$(lr)</span><span class="o" style="font-weight: 600;">))</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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144
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="make"></span>
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Graph file format</span></span>
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146
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="make"><span class="nv" style="color: teal;">graph</span><span class="o" style="font-weight: 600;">?=</span>dot</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">@@ -287,13 +306,16 @@ $(foreach i,$(pe),$(eval $i_n?=$n))</td>
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287
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">override</span> <span class="nv" style="color: teal;">deopt</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$v</span> <span class="nv" style="color: teal;">$(dbopt)</span> <span class="nt" style="color: navy;">-j</span><span class="nv" style="color: teal;">$j</span> <span class="nt" style="color: navy;">-k</span><span class="nv" style="color: teal;">$k</span> <span class="nv" style="color: teal;">$(DISTANCEEST_OPTIONS)</span> <span class="nt" style="color: navy;">-l</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: teal;">$*</span>_l<span class="o" style="font-weight: 600;">)</span> <span class="nt" style="color: navy;">-s</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: teal;">$*</span>_s<span class="o" style="font-weight: 600;">)</span> <span class="nt" style="color: navy;">-n</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: teal;">$*</span>_n<span class="o" style="font-weight: 600;">)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: teal;">$*</span>_de<span class="o" style="font-weight: 600;">)</span></span>
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288
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="make"></span>
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289
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># SimpleGraph parameters</span></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="make"><span class="nv" style="color: teal;">sgopt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: teal;">$(dbopt)</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="make"><span class="nv" style="color: teal;">sgopt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: teal;">$(dbopt)</span><span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">-s</span></span><span class="nv" style="color: teal;"><span class="idiff">$s</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-n</span></span><span class="nv" style="color: teal;"><span class="idiff right">$n</span></span></span>
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291
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">d</span></span>
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292
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="make"><span class="nv" style="color: teal;">sgopt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-d</span><span class="nv" style="color: teal;">$d</span></span>
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293
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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294
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="make"></span>
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295
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># MergePaths parameters</span></span>
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296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="make"><span class="nv" style="color: teal;">mpopt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: teal;">$v</span> <span class="nv" style="color: teal;">$(dbopt)</span> <span class="nt" style="color: navy;">-j</span><span class="nv" style="color: teal;">$j</span> <span class="nt" style="color: navy;">-k</span><span class="nv" style="color: teal;">$k</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="make"><span class="nv" style="color: teal;">mpopt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: teal;">$v</span> <span class="nv" style="color: teal;">$(dbopt)</span> <span class="nt" style="color: navy;">-j</span><span class="nv" style="color: teal;">$j</span> <span class="nt" style="color: navy;">-k</span><span class="nv" style="color: teal;">$k</span> <span class="nt" style="color: navy;">-s</span><span class="nv" style="color: teal;">$s</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">G</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="make"><span class="nv" style="color: teal;">mpopt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-G</span><span class="nv" style="color: teal;">$G</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="make"></span>
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298
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># PathOverlap parameters</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="make"><span class="nv" style="color: teal;">poopt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: teal;">$v</span> <span class="nv" style="color: teal;">$(dbopt)</span> <span class="nt" style="color: navy;">-k</span><span class="nv" style="color: teal;">$k</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -346,9 +368,9 @@ ifndef k</td>
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="make"><span class="nl">error</span><span class="o" style="font-weight: 600;">::</span></span>
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347
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="make"> <span class="p">@</span><span class="o" style="font-weight: 600;">></span>&2 <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'abyss-pe: missing parameter `k`'</span></span>
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348
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(lib)$(in)$(se),)</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(lib)$(in)$(se)<span class="idiff left right">$(lr)</span>,)</span></span>
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350
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="make"><span class="nl">error</span><span class="o" style="font-weight: 600;">::</span></span>
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351
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="make"> <span class="p">@</span><span class="o" style="font-weight: 600;">></span>&2 <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'abyss-pe: missing parameter `lib`, `in`<span class="idiff left right"> or `se</span>`'</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="make"> <span class="p">@</span><span class="o" style="font-weight: 600;">></span>&2 <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'abyss-pe: missing parameter `lib`, `in`<span class="idiff left right">, `se`, or `lr</span>`'</span></span>
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352
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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353
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="make"></span>
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354
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="make"><span class="nl">default</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="371" style="width: 35px; color: rgba(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="393" style="width: 35px; color: rgba(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">@@ -371,7 +393,7 @@ help:</td>
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371
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users@bcgsc.ca.'</span></span>
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372
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="make"></span>
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373
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="make"><span class="nl">version</span><span class="o" style="font-weight: 600;">:</span></span>
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374
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"abyss-pe (ABySS) 2.<span class="idiff left right">0.3</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"abyss-pe (ABySS) 2.<span class="idiff left right">1.0</span>"</span></span>
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Written by Shaun Jackman and Anthony Raymond."</span></span>
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376
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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377
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Copyright 2012 Canada's Michael Smith Genome Science Centre"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="689" style="width: 35px; color: rgba(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="711" style="width: 35px; color: rgba(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">@@ -689,9 +711,106 @@ endif</td>
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689
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711
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="make"><span class="nl">%-8.$g</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%-7.$g %-7.path</span></span>
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690
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712
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="make"> PathOverlap <span class="nt" style="color: navy;">--overlap</span> <span class="nv" style="color: teal;">$(poopt)</span> <span class="nt" style="color: navy;">--</span><span class="nv" style="color: teal;">$g</span> <span class="nv" style="color: teal;">$^</span> <span class="o" style="font-weight: 600;">></span><span class="nv" style="color: teal;">$@</span></span>
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691
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713
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Scaffold using linked reads</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">lr</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="make"></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Tigmint</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="make"></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Options for mapping the reads to the draft assembly.</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="make"><span class="nv" style="color: teal;">lr_l</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$l</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">override</span> <span class="nv" style="color: teal;">lrmapopt</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$v</span> <span class="nt" style="color: navy;">-j</span><span class="nv" style="color: teal;">$j</span> <span class="nt" style="color: navy;">-l</span><span class="nv" style="color: teal;">$(lr_l)</span> <span class="nv" style="color: teal;">$(LR_MAP_OPTIONS)</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="make"></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Options for abyss-scaffold</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="make"><span class="nv" style="color: teal;">lr_s</span><span class="o" style="font-weight: 600;">=</span>1000-100000</span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="make"><span class="nv" style="color: teal;">lr_n</span><span class="o" style="font-weight: 600;">=</span>5-20</span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="make"></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Minimum AS/Read length ratio</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="make"><span class="nv" style="color: teal;">tigmint_as</span><span class="o" style="font-weight: 600;">=</span>0.65</span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="make"></span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Maximum number of mismatches</span></span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="make"><span class="nv" style="color: teal;">tigmint_nm</span><span class="o" style="font-weight: 600;">=</span>5</span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="make"></span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Minimum mapping quality threshold</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="make"><span class="nv" style="color: teal;">tigmint_mapq</span><span class="o" style="font-weight: 600;">=</span>0</span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Maximum distance between reads to be considered the same molecule</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="make"><span class="nv" style="color: teal;">tigmint_d</span><span class="o" style="font-weight: 600;">=</span>50000</span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="make"></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Minimum number of spanning molecules</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="make"><span class="nv" style="color: teal;">tigmint_n</span><span class="o" style="font-weight: 600;">=</span>10</span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="make"></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Size of the window that must be spanned by moecules</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="make"><span class="nv" style="color: teal;">tigmint_w</span><span class="o" style="font-weight: 600;">=</span>1000</span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Align paired-end reads to the draft genome, sort by BX tag,</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># and create molecule extents BED.</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="make"><span class="nl">%.lr.bed</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.fa</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="make"> <span class="nv" style="color: teal;">$(gtime)</span> <span class="nv" style="color: teal;">$(align)</span> <span class="nv" style="color: teal;">$(lrmapopt)</span> <span class="nv" style="color: teal;">$(lr_reads)</span> <span class="nv" style="color: teal;">$<</span> <span class="se" style="color: #d14;">\</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="make"> | samtools sort -@<span class="nv" style="color: teal;">$j</span> <span class="nt" style="color: navy;">-tBX</span> <span class="nt" style="color: navy;">-l0</span> <span class="nt" style="color: navy;">-T</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$$</span><span class="o" style="font-weight: 600;">(</span>mktemp <span class="nt" style="color: navy;">-u</span> <span class="nt" style="color: navy;">-t</span> <span class="nv" style="color: teal;">$@</span>.XXXXXX<span class="o" style="font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="make"> | tigmint-molecule <span class="nt" style="color: navy;">-a</span> <span class="nv" style="color: teal;">$(tigmint_as)</span> <span class="nt" style="color: navy;">-n</span> <span class="nv" style="color: teal;">$(tigmint_nm)</span> <span class="nt" style="color: navy;">-q</span> <span class="nv" style="color: teal;">$(tigmint_mapq)</span> <span class="nt" style="color: navy;">-d</span> <span class="nv" style="color: teal;">$(tigmint_d)</span> - <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="make"> | sort <span class="nt" style="color: navy;">-k1</span>,1 <span class="nt" style="color: navy;">-k2</span>,2n <span class="nt" style="color: navy;">-k3</span>,3n <span class="o" style="font-weight: 600;">></span><span class="nv" style="color: teal;">$@</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Align paired-end reads to the draft genome and sort by BX tag.</span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="make"><span class="nl">%.lr.sortbx.bam</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.fa</span></span>
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="make"> <span class="nv" style="color: teal;">$(gtime)</span> <span class="nv" style="color: teal;">$(align)</span> <span class="nv" style="color: teal;">$(lrmapopt)</span> <span class="nv" style="color: teal;">$(lr_reads)</span> <span class="nv" style="color: teal;">$<</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="make"> | samtools sort -@<span class="nv" style="color: teal;">$j</span> <span class="nt" style="color: navy;">-tBX</span> <span class="nt" style="color: navy;">-T</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$$</span><span class="o" style="font-weight: 600;">(</span>mktemp <span class="nt" style="color: navy;">-u</span> <span class="nt" style="color: navy;">-t</span> <span class="nv" style="color: teal;">$@</span>.XXXXXX<span class="o" style="font-weight: 600;">)</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$@</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Filter the BAM file, create molecule extents BED.</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="make"><span class="nl">%.lr.bed</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.lr.sortbx.bam</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="make"> <span class="nv" style="color: teal;">$(gtime)</span> tigmint-molecule <span class="nt" style="color: navy;">-a</span> <span class="nv" style="color: teal;">$(tigmint_as)</span> <span class="nt" style="color: navy;">-n</span> <span class="nv" style="color: teal;">$(tigmint_nm)</span> <span class="nt" style="color: navy;">-q</span> <span class="nv" style="color: teal;">$(tigmint_mapq)</span> <span class="nt" style="color: navy;">-d</span> <span class="nv" style="color: teal;">$(tigmint_d)</span> <span class="nv" style="color: teal;">$<</span> <span class="se" style="color: #d14;">\</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="make"> | sort <span class="nt" style="color: navy;">-k1</span>,1 <span class="nt" style="color: navy;">-k2</span>,2n <span class="nt" style="color: navy;">-k3</span>,3n <span class="o" style="font-weight: 600;">></span><span class="nv" style="color: teal;">$@</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="make"></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Cut sequences at assembly errors.</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="make"><span class="nl">%.tigmint.fa</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.lr.bed %.fa %.fa.fai</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="make"> <span class="nv" style="color: teal;">$(gtime)</span> tigmint-cut <span class="nt" style="color: navy;">-p</span><span class="nv" style="color: teal;">$j</span> <span class="nt" style="color: navy;">-n</span><span class="nv" style="color: teal;">$(tigmint_n)</span> <span class="nt" style="color: navy;">-w</span><span class="nv" style="color: teal;">$(tigmint_w)</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$@</span> <span class="nv" style="color: teal;">$*</span>.fa <span class="nv" style="color: teal;">$<</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="make"></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># ARCS</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="make"><span class="nv" style="color: teal;">arcs_c</span><span class="o" style="font-weight: 600;">=</span>2</span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="make"><span class="nv" style="color: teal;">arcs_d</span><span class="o" style="font-weight: 600;">=</span>0</span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="make"><span class="nv" style="color: teal;">arcs_e</span><span class="o" style="font-weight: 600;">=</span>30000</span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="make"><span class="nv" style="color: teal;">arcs_l</span><span class="o" style="font-weight: 600;">=</span>0</span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="make"><span class="nv" style="color: teal;">arcs_m</span><span class="o" style="font-weight: 600;">=</span>4-20000</span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="make"><span class="nv" style="color: teal;">arcs_r</span><span class="o" style="font-weight: 600;">=</span>0.05</span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="make"><span class="nv" style="color: teal;">arcs_s</span><span class="o" style="font-weight: 600;">=</span>98</span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="make"><span class="nv" style="color: teal;">arcs_z</span><span class="o" style="font-weight: 600;">=</span>500</span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="make"></span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Align reads and create a graph of linked contigs using ARCS.</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="make"><span class="nl">%.arcs.dist.gv</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.fa</span></span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="make"> <span class="nv" style="color: teal;">$(gtime)</span> <span class="nv" style="color: teal;">$(align)</span> <span class="nv" style="color: teal;">$(lrmapopt)</span> <span class="nv" style="color: teal;">$(lr_reads)</span> <span class="nv" style="color: teal;">$<</span> <span class="se" style="color: #d14;">\</span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="make"> | abyss-fixmate-ssq <span class="nt" style="color: navy;">--all</span> <span class="nt" style="color: navy;">--qname</span> <span class="nv" style="color: teal;">$v</span> <span class="nt" style="color: navy;">-l</span><span class="nv" style="color: teal;">$(lr_l)</span> <span class="nv" style="color: teal;">$(FIXMATE_OPTIONS)</span> <span class="se" style="color: #d14;">\</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="make"> | arcs <span class="nv" style="color: teal;">$v</span> <span class="nt" style="color: navy;">-c</span><span class="nv" style="color: teal;">$(arcs_c)</span> <span class="nt" style="color: navy;">-d</span><span class="nv" style="color: teal;">$(arcs_d)</span> <span class="nt" style="color: navy;">-e</span><span class="nv" style="color: teal;">$(arcs_e)</span> <span class="nt" style="color: navy;">-l</span><span class="nv" style="color: teal;">$(arcs_l)</span> <span class="nt" style="color: navy;">-m</span><span class="nv" style="color: teal;">$(arcs_m)</span> <span class="nt" style="color: navy;">-r</span><span class="nv" style="color: teal;">$(arcs_r)</span> <span class="nt" style="color: navy;">-s</span><span class="nv" style="color: teal;">$(arcs_s)</span> <span class="nt" style="color: navy;">-z</span><span class="nv" style="color: teal;">$(arcs_z)</span> <span class="se" style="color: #d14;">\</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="make"> <span class="nt" style="color: navy;">-g</span> <span class="nv" style="color: teal;">$*</span>.arcs.dist.gv <span class="nt" style="color: navy;">--tsv</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$*</span>.arcs.tsv <span class="nt" style="color: navy;">--barcode-counts</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$*</span>.arcs.barcode-counts.tsv /dev/stdin</span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="make"></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Align paired-end reads to the draft genome and do not sort.</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="make"><span class="nl">%.lr.sortn.sam.gz</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.fa</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="make"> <span class="nv" style="color: teal;">$(gtime)</span> <span class="nv" style="color: teal;">$(align)</span> <span class="nv" style="color: teal;">$(lrmapopt)</span> <span class="nv" style="color: teal;">$(lr_reads)</span> <span class="nv" style="color: teal;">$<</span> <span class="se" style="color: #d14;">\</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="make"> | abyss-fixmate <span class="nt" style="color: navy;">--all</span> <span class="nt" style="color: navy;">--qname</span> <span class="nv" style="color: teal;">$v</span> <span class="nt" style="color: navy;">-l</span><span class="nv" style="color: teal;">$(lr_l)</span> <span class="nv" style="color: teal;">$(FIXMATE_OPTIONS)</span> <span class="se" style="color: #d14;">\</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="make"> | <span class="nv" style="color: teal;">$(gzip)</span> <span class="o" style="font-weight: 600;">></span><span class="nv" style="color: teal;">$@</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="make"></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Create a graph of linked contigs using ARCS.</span></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="make"><span class="nl">%.arcs.dist.gv</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.lr.sortn.sam.gz</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="make"> gunzip <span class="nt" style="color: navy;">-c</span> <span class="nv" style="color: teal;">$<</span> <span class="se" style="color: #d14;">\</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="make"> | arcs <span class="nv" style="color: teal;">$v</span> <span class="nt" style="color: navy;">-c</span><span class="nv" style="color: teal;">$(arcs_c)</span> <span class="nt" style="color: navy;">-d</span><span class="nv" style="color: teal;">$(arcs_d)</span> <span class="nt" style="color: navy;">-e</span><span class="nv" style="color: teal;">$(arcs_e)</span> <span class="nt" style="color: navy;">-l</span><span class="nv" style="color: teal;">$(arcs_l)</span> <span class="nt" style="color: navy;">-m</span><span class="nv" style="color: teal;">$(arcs_m)</span> <span class="nt" style="color: navy;">-r</span><span class="nv" style="color: teal;">$(arcs_r)</span> <span class="nt" style="color: navy;">-s</span><span class="nv" style="color: teal;">$(arcs_s)</span> <span class="nt" style="color: navy;">-z</span><span class="nv" style="color: teal;">$(arcs_z)</span> <span class="se" style="color: #d14;">\</span></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="make"> <span class="nt" style="color: navy;">-g</span> <span class="nv" style="color: teal;">$*</span>.arcs.dist.gv <span class="nt" style="color: navy;">--tsv</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$*</span>.arcs.tsv <span class="nt" style="color: navy;">--barcode-counts</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$*</span>.arcs.barcode-counts.tsv /dev/stdin</span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="make"></span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Scaffold using ARCS and abyss-scaffold.</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="make"><span class="nl">%.arcs.path</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.arcs.dist.gv</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="make"> abyss-scaffold <span class="nv" style="color: teal;">$(scopt)</span> <span class="nt" style="color: navy;">-s</span><span class="nv" style="color: teal;">$(lr_s)</span> <span class="nt" style="color: navy;">-n</span><span class="nv" style="color: teal;">$(lr_n)</span> <span class="nt" style="color: navy;">-g</span> <span class="nv" style="color: teal;">$@</span>.dot <span class="nv" style="color: teal;">$(LR_SCAFFOLD_OPTIONS)</span> <span class="nv" style="color: teal;">$<</span> <span class="o" style="font-weight: 600;">></span><span class="nv" style="color: teal;">$@</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="make"></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Create the FASTA file of ARCS scaffolds.</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="make"><span class="nl">%.arcs.fa</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.fa %.arcs.path</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="make"> MergeContigs <span class="nv" style="color: teal;">$(mcopt)</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$@</span> <span class="nv" style="color: teal;">$^</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="make"></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="make"><span class="nl">%-scaffolds.fa</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%-8.tigmint.arcs.fa</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="make"> ln <span class="nt" style="color: navy;">-sf</span> <span class="nv" style="color: teal;">$<</span> <span class="nv" style="color: teal;">$@</span></span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="make"></span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="make"></span>
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809
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="make"><span class="nl">%-scaffolds.fa</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%-8.fa</span></span>
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693
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="make"> ln <span class="nt" style="color: navy;">-sf</span> <span class="nv" style="color: teal;">$<</span> <span class="nv" style="color: teal;">$@</span></span>
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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="make"></span>
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="make"><span class="nl">%-scaffolds.$g</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%-8.$g</span></span>
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815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="make"> ln <span class="nt" style="color: navy;">-sf</span> <span class="nv" style="color: teal;">$<</span> <span class="nv" style="color: teal;">$@</span></span>
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="make"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -854,4 +973,4 @@ env:</td>
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854
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973
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<pre style="margin: 0;"> <span id="LC973" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'[override], if variable was defined with an override directive in (this) makefile.'</span></span>
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855
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974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="make"></span>
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856
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975
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<pre style="margin: 0;"> <span id="LC975" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@$(foreach</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">var,$(varList),\</span></span>
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857
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<pre style="margin: 0;">-<span id="LC857" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">echo</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-e</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(var)</span><span class="s2" style="color: #d14;">" = "</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$($(var))</span><span class="s2" style="color: #d14;">"\t["</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$(origin</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(var))</span><span class="s2" style="color: #d14;">"]"</span><span class="idiff left"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">|</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">grep</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">-v</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff right">"undefined"</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">;)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">echo</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-e</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(var)</span><span class="s2" style="color: #d14;">" = "</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$($(var))</span><span class="s2" style="color: #d14;">"\t["</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$(origin</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(var))</span><span class="s2" style="color: #d14;">"]"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">;)</span></span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">AC_PREREQ(2.62)</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">AC_INIT(ABySS, 2.<span class="idiff left right">0.3</span>, abyss-users@bcgsc.ca, abyss,</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">AC_INIT(ABySS, 2.<span class="idiff left right">1.0</span>, abyss-users@bcgsc.ca, abyss,</span>
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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">m4_include(m4/m4_ax_pthread.m4)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">AM_INIT_AUTOMAKE(1.9.6 foreign subdir-objects)</span>
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<a href="https://salsa.debian.org/med-team/abyss/commit/e2ac24df5fbe2bfbc5e90d8f8536715303bda141#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.<span class="idiff left right">0.3</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.<span class="idiff left right">1.0</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/commit/e2ac24df5fbe2bfbc5e90d8f8536715303bda141#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.<span class="idiff left right">0.3</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.<span class="idiff left right">1.0</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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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH abyss-tofastq "1" "2015-May" "ABySS 2.<span class="idiff left right">0.3</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.<span class="idiff left right">1.0</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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